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Protein

Genome polyprotein

Gene
N/A
Organism
Hepatitis C virus genotype 1a (isolate H) (HCV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core protein packages viral RNA to form a viral nucleocapsid, and promotes virion budding. Modulates viral translation initiation by interacting with HCV IRES and 40S ribosomal subunit. Also regulates many host cellular functions such as signaling pathways and apoptosis. Prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma signaling pathways and by inducing human STAT1 degradation. Thought to play a role in virus-mediated cell transformation leading to hepatocellular carcinomas. Interacts with, and activates STAT3 leading to cellular transformation. May repress the promoter of p53, and sequester CREB3 and SP110 isoform 3/Sp110b in the cytoplasm. Also represses cell cycle negative regulating factor CDKN1A, thereby interrupting an important check point of normal cell cycle regulation. Targets transcription factors involved in the regulation of inflammatory responses and in the immune response: suppresses NK-kappaB activation, and activates AP-1. Could mediate apoptotic pathways through association with TNF-type receptors TNFRSF1A and LTBR, although its effect on death receptor-induced apoptosis remains controversial. Enhances TRAIL mediated apoptosis, suggesting that it might play a role in immune-mediated liver cell injury. Seric core protein is able to bind C1QR1 at the T-cell surface, resulting in down-regulation of T-lymphocytes proliferation. May transactivate human MYC, Rous sarcoma virus LTR, and SV40 promoters. May suppress the human FOS and HIV-1 LTR activity. Alters lipid metabolism by interacting with hepatocellular proteins involved in lipid accumulation and storage. Core protein induces up-regulation of FAS promoter activity, and thereby probably contributes to the increased triglyceride accumulation in hepatocytes (steatosis) (By similarity).By similarity
E1 and E2 glycoproteins form a heterodimer that is involved in virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane. E1/E2 heterodimer binds to human LDLR, CD81 and SCARB1/SR-BI receptors, but this binding is not sufficient for infection, some additional liver specific cofactors may be needed. The fusion function may possibly be carried by E1. E2 inhibits human EIF2AK2/PKR activation, preventing the establishment of an antiviral state. E2 is a viral ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on liver sinusoidal endothelial cells and macrophage-like cells of lymph node sinuses. These interactions allow capture of circulating HCV particles by these cells and subsequent transmission to permissive cells. DCs act as sentinels in various tissues where they entrap pathogens and convey them to local lymphoid tissue or lymph node for establishment of immunity. Capture of circulating HCV particles by these SIGN+ cells may facilitate virus infection of proximal hepatocytes and lymphocyte subpopulations and may be essential for the establishment of persistent infection (By similarity).By similarity
P7 seems to be a heptameric ion channel protein (viroporin) and is inhibited by the antiviral drug amantadine (By similarity). Also inhibited by long-alkyl-chain iminosugar derivatives. Essential for infectivity.By similarity1 Publication
Protease NS2-3 is a cysteine protease responsible for the autocatalytic cleavage of NS2-NS3. Seems to undergo self-inactivation following maturation (By similarity).By similarity
NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS4A, is responsible for the cleavages of NS3-NS4A, NS4A-NS4B, NS4B-NS5A and NS5A-NS5B. NS3/NS4A complex also prevents phosphorylation of human IRF3, thus preventing the establishment of dsRNA induced antiviral state. NS3 RNA helicase binds to RNA and unwinds dsRNA in the 3' to 5' direction, and likely RNA stable secondary structure in the template strand (By similarity). Cleaves and inhibits the host antiviral protein MAVS.By similarity1 Publication
NS4B induces a specific membrane alteration that serves as a scaffold for the virus replication complex. This membrane alteration gives rise to the so-called ER-derived membranous web that contains the replication complex. NS4B polymerization or in protein-protein interactions activity may contribute to its function in membranous web formation.1 Publication
NS5A is a component of the replication complex involved in RNA-binding. Its interaction with Human VAPB may target the viral replication complex to vesicles. Down-regulates viral IRES translation initiation. Mediates interferon resistance, presumably by interacting with and inhibiting human EIF2AK2/PKR. Seems to inhibit apoptosis by interacting with BIN1 and FKBP8. The hyperphosphorylated form of NS5A is an inhibitor of viral replication (By similarity).By similarity
NS5B is an RNA-dependent RNA polymerase that plays an essential role in the virus replication.1 Publication

Catalytic activityi

Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
NTP + H2O = NDP + phosphate.
ATP + H2O = ADP + phosphate.

Cofactori

Protein has several cofactor binding sites:
  • Zn2+By similarityNote: Binds 1 zinc ion per NS3 protease domain.By similarity
  • Zn2+By similarityNote: Binds 1 zinc ion per NS5A N-terminal domain.By similarity

Enzyme regulationi

Activity of auto-protease NS2-3 is dependent on zinc ions and completely inhibited by EDTA. Serine protease NS3 is also activated by zinc ions (By similarity). Activity is up-regulated by PKN2-mediated phosphorylation.By similarity1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei952For protease NS2-3 activity; shared with dimeric partner1
Active sitei972For protease NS2-3 activity; shared with dimeric partner1
Active sitei993For protease NS2-3 activity; shared with dimeric partner1
Active sitei1083Charge relay system; for serine protease NS3 activityBy similarity1
Active sitei1107Charge relay system; for serine protease NS3 activityBy similarity1
Metal bindingi1123Zinc1
Metal bindingi1125Zinc1
Active sitei1165Charge relay system; for serine protease NS3 activity1
Metal bindingi1171Zinc1
Metal bindingi1175Zinc1
Metal bindingi2011ZincBy similarity1
Metal bindingi2029ZincBy similarity1
Metal bindingi2031ZincBy similarity1
Metal bindingi2052ZincBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1230 – 1237ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATPase activity Source: AgBase
  • ATPase regulator activity Source: AgBase
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent helicase activity Source: InterPro
  • cysteine-type endopeptidase activity Source: InterPro
  • DEAD/H-box RNA helicase binding Source: AgBase
  • enzyme binding Source: AgBase
  • heat shock protein binding Source: AgBase
  • identical protein binding Source: IntAct
  • ion channel activity Source: UniProtKB-KW
  • keratin filament binding Source: AgBase
  • kinase binding Source: AgBase
  • MHC class I protein binding Source: AgBase
  • p53 binding Source: AgBase
  • peptidase activity Source: AgBase
  • protein phosphatase binding Source: AgBase
  • Rab GTPase binding Source: AgBase
  • RNA binding Source: UniProtKB-KW
  • RNA-directed RNA polymerase activity Source: AgBase
  • scavenger receptor binding Source: AgBase
  • serine-type endopeptidase activity Source: AgBase
  • serine-type peptidase activity Source: AgBase
  • STAT family protein binding Source: AgBase
  • structural molecule activity Source: InterPro
  • Toll-like receptor 2 binding Source: AgBase
  • transcription factor binding Source: AgBase
  • translation initiation factor binding Source: AgBase
  • zinc ion binding Source: AgBase

GO - Biological processi

  • clathrin-dependent endocytosis of virus by host cell Source: UniProtKB-KW
  • fusion of virus membrane with host endosome membrane Source: UniProtKB-KW
  • induction by virus of host autophagy Source: UniProtKB-KW
  • lymphocyte aggregation Source: AgBase
  • modulation by virus of host G1/S transition checkpoint Source: UniProtKB-KW
  • modulation by virus of host protein transport Source: AgBase
  • modulation by virus of host transcription Source: AgBase
  • negative regulation by symbiont of host defense-related protein level Source: AgBase
  • negative regulation by symbiont of host protein levels Source: AgBase
  • negative regulation of acute inflammatory response Source: AgBase
  • negative regulation of ATPase activity Source: AgBase
  • negative regulation of B cell proliferation Source: AgBase
  • negative regulation of cell death Source: AgBase
  • negative regulation of defense response to virus by host Source: AgBase
  • negative regulation of endoplasmic reticulum unfolded protein response Source: AgBase
  • negative regulation of endoribonuclease activity Source: AgBase
  • negative regulation of execution phase of apoptosis Source: AgBase
  • negative regulation of interleukin-6-mediated signaling pathway Source: AgBase
  • negative regulation of interleukin-6 production Source: AgBase
  • negative regulation of kinase activity Source: AgBase
  • negative regulation of protein autophosphorylation Source: AgBase
  • negative regulation of protein secretion Source: AgBase
  • negative regulation of release of cytochrome c from mitochondria Source: AgBase
  • negative regulation of RNA interference Source: AgBase
  • negative regulation of toll-like receptor 2 signaling pathway Source: AgBase
  • negative regulation of toll-like receptor 4 signaling pathway Source: AgBase
  • negative regulation of toll-like receptor 7 signaling pathway Source: AgBase
  • negative regulation of toll-like receptor 9 signaling pathway Source: AgBase
  • negative regulation of transcription from RNA polymerase II promoter Source: AgBase
  • negative regulation of tumor necrosis factor-mediated signaling pathway Source: AgBase
  • negative regulation of tyrosine phosphorylation of Stat1 protein Source: AgBase
  • pore formation by virus in membrane of host cell Source: UniProtKB-KW
  • positive regulation by symbiont of host protein levels Source: AgBase
  • positive regulation by symbiont of host transcription Source: AgBase
  • positive regulation of alkaline phosphatase activity Source: AgBase
  • positive regulation of cell growth Source: AgBase
  • positive regulation of cell proliferation Source: AgBase
  • positive regulation of cytokinesis Source: AgBase
  • positive regulation of gene expression Source: AgBase
  • positive regulation of I-kappaB phosphorylation Source: AgBase
  • positive regulation of proteolysis Source: AgBase
  • positive regulation of secretion Source: AgBase
  • positive regulation of translation Source: AgBase
  • positive regulation of tumor necrosis factor-mediated signaling pathway Source: AgBase
  • positive regulation of viral process Source: AgBase
  • protein localization to lipid particle Source: AgBase
  • protein oligomerization Source: UniProtKB-KW
  • regulation of endoplasmic reticulum unfolded protein response Source: AgBase
  • suppression by virus of host apoptotic process Source: AgBase
  • suppression by virus of host intracellular interferon activity Source: AgBase
  • suppression by virus of host IRF9 activity Source: AgBase
  • suppression by virus of host MAVS activity Source: UniProtKB-KW
  • suppression by virus of host MAVS activity by MAVS proteolysis Source: AgBase
  • suppression by virus of host NF-kappaB transcription factor activity Source: AgBase
  • suppression by virus of host PKR activity Source: AgBase
  • suppression by virus of host protein phosphorylation Source: AgBase
  • suppression by virus of host STAT1 activity by positive regulation of STAT1 catabolic process Source: AgBase
  • suppression by virus of host TRAF activity Source: AgBase
  • suppression by virus of host transcription Source: AgBase
  • suppression by virus of host translation initiation factor activity by induction of host protein dephosphorylation Source: AgBase
  • suppression by virus of host type I interferon-mediated signaling pathway Source: AgBase
  • transcription, DNA-templated Source: UniProtKB-KW
  • transformation of host cell by virus Source: InterPro
  • translocation of peptides or proteins into host cell cytoplasm Source: AgBase
  • viral budding from ER membrane Source: UniProtKB
  • viral protein processing Source: AgBase
  • viral RNA genome replication Source: InterPro
  • virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Ion channel, Nucleotidyltransferase, Protease, Ribonucleoprotein, RNA-directed RNA polymerase, Serine protease, Thiol protease, Transferase, Viral ion channel

Keywords - Biological processi

Activation of host autophagy by virus, Apoptosis, Clathrin-mediated endocytosis of virus by host, Fusion of virus membrane with host endosomal membrane, Fusion of virus membrane with host membrane, G1/S host cell cycle checkpoint dysregulation by virus, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host interferon signaling pathway by virus, Inhibition of host MAVS by virus, Inhibition of host RLR pathway by virus, Inhibition of host STAT1 by virus, Inhibition of host TRAFs by virus, Interferon antiviral system evasion, Ion transport, Modulation of host cell cycle by virus, Transcription, Transcription regulation, Transport, Viral attachment to host cell, Viral immunoevasion, Viral penetration into host cytoplasm, Viral RNA replication, Virus endocytosis by host, Virus entry into host cell

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Viral nucleoprotein, Zinc

Enzyme and pathway databases

BRENDAi3.4.21.98. 2642.
3.6.4.13. 2642.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 11 chains:
Alternative name(s):
Capsid protein C
p21
Alternative name(s):
gp32
gp35
Alternative name(s):
NS1
gp68
gp70
Protease NS2-3 (EC:3.4.22.-)
Short name:
p23
Alternative name(s):
Hepacivirin
NS3P
p70
Alternative name(s):
p8
Alternative name(s):
p27
Alternative name(s):
p56
Alternative name(s):
NS5B
p68
OrganismiHepatitis C virus genotype 1a (isolate H) (HCV)
Taxonomic identifieri11108 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageFlaviviridaeHepacivirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000000518 Componenti: Genome

Subcellular locationi

Core protein p21 :
Core protein p19 :
Envelope glycoprotein E1 :
  • Virion membrane Curated; Single-pass type I membrane protein Curated
  • Host endoplasmic reticulum membrane; Single-pass type I membrane protein

  • Note: The C-terminal transmembrane domain acts as a signal sequence and forms a hairpin structure before cleavage by host signal peptidase. After cleavage, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor. A reorientation of the second hydrophobic stretch occurs after cleavage producing a single reoriented transmembrane domain. These events explain the final topology of the protein. ER retention of E1 is leaky and, in overexpression conditions, only a small fraction reaches the plasma membrane.
Envelope glycoprotein E2 :
  • Virion membrane Curated; Single-pass type I membrane protein Curated
  • Host endoplasmic reticulum membrane; Single-pass type I membrane protein

  • Note: The C-terminal transmembrane domain acts as a signal sequence and forms a hairpin structure before cleavage by host signal peptidase. After cleavage, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor. A reorientation of the second hydrophobic stretch occurs after cleavage producing a single reoriented transmembrane domain. These events explain the final topology of the protein. ER retention of E2 is leaky and, in overexpression conditions, only a small fraction reaches the plasma membrane.
p7 :
Serine protease NS3 :
Non-structural protein 4A :
Non-structural protein 4B :
RNA-directed RNA polymerase :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini2 – 168CytoplasmicSequence analysisAdd BLAST167
Transmembranei169 – 189HelicalSequence analysisAdd BLAST21
Topological domaini190 – 358LumenalSequence analysisAdd BLAST169
Transmembranei359 – 379HelicalSequence analysisAdd BLAST21
Topological domaini380 – 725LumenalSequence analysisAdd BLAST346
Transmembranei726 – 746HelicalSequence analysisAdd BLAST21
Topological domaini747 – 757LumenalSequence analysisAdd BLAST11
Transmembranei758 – 778HelicalSequence analysisAdd BLAST21
Topological domaini779 – 782CytoplasmicSequence analysis4
Transmembranei783 – 803HelicalSequence analysisAdd BLAST21
Topological domaini804 – 813LumenalSequence analysis10
Transmembranei814 – 834HelicalSequence analysisAdd BLAST21
Topological domaini835 – 881CytoplasmicSequence analysisAdd BLAST47
Transmembranei882 – 902HelicalSequence analysisAdd BLAST21
Topological domaini903 – 928LumenalSequence analysisAdd BLAST26
Transmembranei929 – 949HelicalSequence analysisAdd BLAST21
Topological domaini950 – 1657CytoplasmicSequence analysisAdd BLAST708
Transmembranei1658 – 1678HelicalSequence analysisAdd BLAST21
Topological domaini1679 – 1805CytoplasmicSequence analysisAdd BLAST127
Transmembranei1806 – 1826HelicalSequence analysisAdd BLAST21
Topological domaini1827 – 1828LumenalSequence analysis2
Transmembranei1829 – 1849HelicalSequence analysisAdd BLAST21
Topological domaini1850CytoplasmicSequence analysis1
Transmembranei1851 – 1871HelicalSequence analysisAdd BLAST21
Topological domaini1872 – 1881LumenalSequence analysis10
Transmembranei1882 – 1902HelicalSequence analysisAdd BLAST21
Topological domaini1903 – 1972CytoplasmicSequence analysisAdd BLAST70
Intramembranei1973 – 2002By similarityAdd BLAST30
Topological domaini2003 – 2990CytoplasmicSequence analysisAdd BLAST988
Transmembranei2991 – 3011HelicalBy similarityAdd BLAST21

GO - Cellular componenti

  • cytoplasmic viral factory Source: UniProtKB
  • extracellular region Source: UniProtKB-SubCell
  • host cell cytoplasm Source: AgBase
  • host cell cytosol Source: AgBase
  • host cell endoplasmic reticulum Source: AgBase
  • host cell endoplasmic reticulum membrane Source: UniProtKB-SubCell
  • host cell Golgi apparatus Source: AgBase
  • host cell lipid particle Source: AgBase
  • host cell membrane Source: AgBase
  • host cell mitochondrial membrane Source: UniProtKB-SubCell
  • host cell nucleus Source: AgBase
  • host cell perinuclear region of cytoplasm Source: AgBase
  • host cell plasma membrane Source: UniProtKB-SubCell
  • host intracellular organelle Source: AgBase
  • integral component of membrane Source: UniProtKB-KW
  • integral to membrane of host cell Source: UniProtKB-KW
  • membrane Source: AgBase
  • viral envelope Source: UniProtKB-KW
  • viral nucleocapsid Source: UniProtKB-KW
  • virion membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host endoplasmic reticulum, Host lipid droplet, Host membrane, Host mitochondrion, Host nucleus, Membrane, Secreted, Viral envelope protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi720V → L: Increases processing between E2 and p7. 1 Publication1
Mutagenesisi779K → I: Virus can no longer infect chimpanzee. 1 Publication1
Mutagenesisi781R → S: Virus can no longer infect chimpanzee. 1 Publication1
Mutagenesisi952H → A: Complete loss of NS2-NS3 cleavage. 2 Publications1
Mutagenesisi993C → A: Complete loss of NS2-NS3 cleavage. 2 Publications1
Mutagenesisi1165S → A: Complete loss of NS3-NS4A, NS4A-NS4B, NS4B-NS5A and NS5A-NS5B cleavages. 1 Publication1
Mutagenesisi1968C → A: Strong decrease in NS4B palmitoylation. 1 Publication1
Mutagenesisi1972C → A: Slight decrease in NS4B palmitoylation. 1 Publication1
Mutagenesisi2321S → A: Loss of phosphorylation. 1 Publication1

Keywords - Diseasei

Oncogene

Chemistry databases

ChEMBLiCHEMBL3638344.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostBy similarity
ChainiPRO_00000375662 – 191Core protein p21Sequence analysisAdd BLAST190
ChainiPRO_00000375672 – 177Core protein p19By similarityAdd BLAST176
PropeptideiPRO_0000037568178 – 191ER anchor for the core protein, removed in mature form by host signal peptidaseBy similarityAdd BLAST14
ChainiPRO_0000037569192 – 383Envelope glycoprotein E1Sequence analysisAdd BLAST192
ChainiPRO_0000037570384 – 746Envelope glycoprotein E2Sequence analysisAdd BLAST363
ChainiPRO_0000037571747 – 809p7Add BLAST63
ChainiPRO_0000037572810 – 1026Protease NS2-3PROSITE-ProRule annotationAdd BLAST217
ChainiPRO_00000375731027 – 1657Serine protease NS3Sequence analysisAdd BLAST631
ChainiPRO_00000375741658 – 1711Non-structural protein 4ASequence analysisAdd BLAST54
ChainiPRO_00000375751712 – 1972Non-structural protein 4BSequence analysisAdd BLAST261
ChainiPRO_00000375761973 – 2420Non-structural protein 5ASequence analysisAdd BLAST448
ChainiPRO_00000375772421 – 3011RNA-directed RNA polymeraseSequence analysisAdd BLAST591

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine; by hostBy similarity1
Modified residuei53Phosphoserine; by hostBy similarity1
Modified residuei99Phosphoserine; by hostBy similarity1
Modified residuei116Phosphoserine; by host PKABy similarity1
Glycosylationi196N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi209N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi234N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi305N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi417N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi423N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi430N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi448N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi476N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi532N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi540N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi556N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi576N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi623N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi645N-linked (GlcNAc...); by hostSequence analysis1
Lipidationi1968S-palmitoyl cysteine; by host1 Publication1
Lipidationi1972S-palmitoyl cysteine; by host; partial1 Publication1
Disulfide bondi2114 ↔ 2162By similarity
Modified residuei2194Phosphoserine; by host; in p56By similarity1
Modified residuei2197Phosphoserine; by host; in p58By similarity1
Modified residuei2201Phosphoserine; by host; in p58By similarity1
Modified residuei2204Phosphoserine; by host; in p58By similarity1
Modified residuei2321Phosphoserine; by host1 Publication1

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases. The core protein is synthesized as a 21 kDa precursor which is retained in the ER membrane through the hydrophobic signal peptide. Cleavage by the signal peptidase releases the 19 kDa mature core protein. The other proteins (p7, NS2-3, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (By similarity).By similarity
Envelope E1 and E2 glycoproteins are highly N-glycosylated.
Core protein is phosphorylated by host PKC and PKA.By similarity
NS5A is phosphorylated in a basal form termed p56. p58 is a hyperphosphorylated form of p56. p56 and p58 coexist in the cell in roughly equivalent amounts. Hyperphosphorylation is dependent on the presence of NS4A. Human AKT1, RPS6KB1/p70S6K, MAP2K1/MEK1, MAP2K6/MKK6 and CSNK1A1/CKI-alpha kinases may be responsible for NS5A phosphorylation (By similarity).By similarity
The N-terminus of a fraction of NS4B molecules seems to be relocated post-translationally from the cytoplasm to the ER lumen, with a 5th transmembrane segment. The C-terminus of NS2 may be lumenal with a fourth transmembrane segment (By similarity).By similarity
Core protein is ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation.By similarity
NS4B is palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei177 – 178Cleavage; by host signal peptidaseBy similarity2
Sitei191 – 192Cleavage; by host signal peptidaseSequence analysis2
Sitei383 – 384Cleavage; by host signal peptidaseSequence analysis2
Sitei746 – 747Cleavage; by host signal peptidase2
Sitei809 – 810Cleavage; by host signal peptidase2
Sitei1026 – 1027Cleavage; by protease NS2-3PROSITE-ProRule annotation2
Sitei1657 – 1658Cleavage; by serine protease NS3Sequence analysis2
Sitei1711 – 1712Cleavage; by serine protease NS3Sequence analysis2
Sitei1972 – 1973Cleavage; by serine protease NS3Sequence analysis2
Sitei2420 – 2421Cleavage; by serine protease NS3Sequence analysis2

Keywords - PTMi

Acetylation, Disulfide bond, Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein, Ubl conjugation

PTM databases

iPTMnetiP27958.

Interactioni

Subunit structurei

Core protein is a homomultimer that binds the C-terminal part of E1 and interacts with numerous cellular proteins. Interacts (via N-terminus finger domain) with human PKN2. Interaction with human STAT1 SH2 domain seems to result in decreased STAT1 phosphorylation, leading to decreased IFN-stimulated gene transcription. In addition to blocking the formation of phosphorylated STAT1, the core protein also promotes ubiquitin-mediated proteasome-dependent degradation of STAT1. Interacts with, and constitutively activates human STAT3. Associates with human LTBR and TNFRSF1A receptors and possibly induces apoptosis. Binds to human SP110 isoform 3/Sp110b, HNRPK, C1QR1, YWHAE, UBE3A/E6AP, DDX3X, APOA2 and RXRA proteins. Interacts with human CREB3 nuclear transcription protein, triggering cell transformation. May interact with human p53. Also binds human cytokeratins KRT8, KRT18, KRT19 and VIM (vimentin). Interacts with human ACY3. E1 and E2 glycoproteins form a heterodimer that binds to human LDLR, CLDN1, CD81 and SCARB1 receptors. E2 binds and inhibits human EIF2AK2/PKR. Also binds human CD209/DC-SIGN and CLEC4M/DC-SIGNR. p7 forms a homoheptamer in vitro. NS2 forms a homodimer containing a pair of composite active sites at the dimerization interface. NS2 seems to interact with all other non-structural (NS) proteins. NS4A interacts with NS3 serine protease and stabilizes its folding. NS3-NS4A complex is essential for the activation of the latter and allows membrane anchorage of NS3. NS3 interacts with human TANK-binding kinase TBK1 and MAVS. NS4B and NS5A form homodimers and seem to interact with all other non-structural (NS) proteins. NS5A also interacts with human EIF2AK2/PKR, FKBP8, GRB2, BIN1, PIK3R1, SRCAP, VAPB and with most Src-family kinases. NS5B is a homooligomer and interacts with human VAPB, HNRNPA1 and SEPT6 (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
P266604EBI-6377335,EBI-6875462From a different organism.
Q99IB83EBI-8753518,EBI-6858513From a different organism.
ACTN1P128147EBI-6904388,EBI-351710From a different organism.
AP2M1Q96CW14EBI-6377335,EBI-297683From a different organism.
APOEP026494EBI-6904269,EBI-1222467From a different organism.
ARAP1Q96P483EBI-8753518,EBI-710003From a different organism.
ATF6BQ999415EBI-8763498,EBI-2841031From a different organism.
ATMQ133153EBI-6904388,EBI-495465From a different organism.
BIN1O0049911EBI-8753518,EBI-719094From a different organism.
BIN1O00499-72EBI-8753518,EBI-8870146From a different organism.
C1QBPQ070214EBI-6377335,EBI-347528From a different organism.
CCDC86Q9H6F53EBI-8753518,EBI-721289From a different organism.
CD81P6003311EBI-6904269,EBI-712921From a different organism.
CDKN1AP389363EBI-6377335,EBI-375077From a different organism.
CHEK2O960173EBI-6904388,EBI-1180783From a different organism.
CIDEBQ9UHD46EBI-6919131,EBI-7062247From a different organism.
CNXQ920L92EBI-6904269,EBI-9209498From a different organism.
CRABP1P297623EBI-8753518,EBI-725950From a different organism.
DDX3XO0057111EBI-6377335,EBI-353779From a different organism.
DDX5P1784412EBI-6904388,EBI-351962From a different organism.
EIF2AK2P195255EBI-8753518,EBI-640775From a different organism.
Eif2ak3Q9Z2B55EBI-6904269,EBI-1226344From a different organism.
EIF4A2Q142404EBI-6904388,EBI-73473From a different organism.
ERC1Q8IUD2-38EBI-3649474,EBI-9352449From a different organism.
ERC1Q8IUD2-43EBI-3649474,EBI-9352501From a different organism.
FGBP026754EBI-6377335,EBI-1034445From a different organism.
FYNP062414EBI-706378,EBI-515315From a different organism.
GRB2P629933EBI-706378,EBI-401755From a different organism.
HCKP086315EBI-706378,EBI-346340From a different organism.
HNRNPA1P096514EBI-6904388,EBI-352662From a different organism.
HSPA5P078233EBI-6904259,EBI-371776From a different organism.
IKBKEQ141642EBI-6919131,EBI-307369From a different organism.
IPO5O004105EBI-8753518,EBI-356424From a different organism.
LckP062403EBI-706378,EBI-1401From a different organism.
LTFP027889EBI-6904269,EBI-1058602From a different organism.
LTFP246273EBI-6904269,EBI-8076910From a different organism.
LYNP079484EBI-706378,EBI-79452From a different organism.
MAPKAPK3Q166445EBI-6377335,EBI-1384657From a different organism.
NCLP193384EBI-6904388,EBI-346967From a different organism.
PI4KAP423567EBI-8753518,EBI-723050From a different organism.
PMLP295906EBI-6377335,EBI-295890From a different organism.
PSMB8P280624EBI-3649474,EBI-372294From a different organism.
SCARB1Q8WTV02EBI-6904269,EBI-78657From a different organism.
SEPT6Q141414EBI-6904388,EBI-745901From a different organism.
SNRPD1P623147EBI-3649474,EBI-372177From a different organism.
STAT1P422242EBI-6377335,EBI-1057697From a different organism.
TBC1D20Q96BZ911EBI-8753518,EBI-9254454From a different organism.
TBK1Q9UHD24EBI-3649474,EBI-356402From a different organism.
TMEM173Q86WV65EBI-8763498,EBI-2800345From a different organism.
TP53BP2Q136255EBI-6377335,EBI-77642From a different organism.
Traf2P394295EBI-8753518,EBI-520016From a different organism.
VAPAQ9P0L07EBI-8753518,EBI-1059156From a different organism.
VIMP086704EBI-6377335,EBI-353844From a different organism.

GO - Molecular functioni

  • DEAD/H-box RNA helicase binding Source: AgBase
  • enzyme binding Source: AgBase
  • heat shock protein binding Source: AgBase
  • identical protein binding Source: IntAct
  • keratin filament binding Source: AgBase
  • kinase binding Source: AgBase
  • MHC class I protein binding Source: AgBase
  • p53 binding Source: AgBase
  • protein phosphatase binding Source: AgBase
  • Rab GTPase binding Source: AgBase
  • scavenger receptor binding Source: AgBase
  • STAT family protein binding Source: AgBase
  • Toll-like receptor 2 binding Source: AgBase
  • transcription factor binding Source: AgBase
  • translation initiation factor binding Source: AgBase

Protein-protein interaction databases

IntActiP27958. 231 interactors.
MINTiMINT-106294.

Chemistry databases

BindingDBiP27958.

Structurei

Secondary structure

13011
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 12Combined sources3
Beta strandi16 – 18Combined sources3
Turni19 – 23Combined sources5
Beta strandi30 – 35Combined sources6
Turni36 – 38Combined sources3
Beta strandi39 – 41Combined sources3
Helixi316 – 323Combined sources8
Beta strandi412 – 414Combined sources3
Beta strandi416 – 418Combined sources3
Beta strandi420 – 422Combined sources3
Beta strandi425 – 427Combined sources3
Turni432 – 435Combined sources4
Helixi436 – 442Combined sources7
Beta strandi496 – 498Combined sources3
Helixi499 – 501Combined sources3
Beta strandi502 – 504Combined sources3
Beta strandi507 – 515Combined sources9
Beta strandi532 – 534Combined sources3
Beta strandi536 – 538Combined sources3
Beta strandi550 – 556Combined sources7
Beta strandi561 – 565Combined sources5
Helixi568 – 571Combined sources4
Turni574 – 577Combined sources4
Beta strandi579 – 581Combined sources3
Beta strandi602 – 604Combined sources3
Beta strandi607 – 609Combined sources3
Helixi614 – 617Combined sources4
Helixi619 – 621Combined sources3
Beta strandi625 – 633Combined sources9
Beta strandi636 – 644Combined sources9
Helixi911 – 923Combined sources13
Turni924 – 927Combined sources4
Helixi931 – 944Combined sources14
Turni951 – 953Combined sources3
Helixi956 – 958Combined sources3
Helixi964 – 967Combined sources4
Turni971 – 974Combined sources4
Beta strandi975 – 977Combined sources3
Beta strandi982 – 984Combined sources3
Turni988 – 990Combined sources3
Beta strandi1000 – 1008Combined sources9
Beta strandi1010 – 1013Combined sources4
Turni1016 – 1018Combined sources3
Helixi1019 – 1021Combined sources3
Beta strandi1032 – 1035Combined sources4
Helixi1039 – 1048Combined sources10
Beta strandi1057 – 1063Combined sources7
Beta strandi1068 – 1074Combined sources7
Beta strandi1077 – 1081Combined sources5
Helixi1082 – 1085Combined sources4
Beta strandi1090 – 1092Combined sources3
Beta strandi1095 – 1097Combined sources3
Beta strandi1100 – 1103Combined sources4
Turni1104 – 1107Combined sources4
Beta strandi1108 – 1112Combined sources5
Beta strandi1128 – 1133Combined sources6
Beta strandi1139 – 1144Combined sources6
Beta strandi1146 – 1157Combined sources12
Helixi1158 – 1160Combined sources3
Turni1161 – 1163Combined sources3
Beta strandi1168 – 1170Combined sources3
Turni1172 – 1174Combined sources3
Beta strandi1176 – 1186Combined sources11
Beta strandi1189 – 1197Combined sources9
Helixi1198 – 1206Combined sources9
Beta strandi1224 – 1226Combined sources3
Turni1236 – 1238Combined sources3
Helixi1239 – 1246Combined sources8
Beta strandi1251 – 1256Combined sources6
Helixi1258 – 1271Combined sources14
Beta strandi1277 – 1280Combined sources4
Beta strandi1283 – 1285Combined sources3
Beta strandi1290 – 1295Combined sources6
Helixi1296 – 1301Combined sources6
Helixi1304 – 1307Combined sources4
Beta strandi1311 – 1316Combined sources6
Turni1317 – 1319Combined sources3
Helixi1323 – 1335Combined sources13
Turni1336 – 1340Combined sources5
Beta strandi1342 – 1347Combined sources6
Beta strandi1362 – 1366Combined sources5
Beta strandi1371 – 1375Combined sources5
Beta strandi1378 – 1380Combined sources3
Helixi1382 – 1385Combined sources4
Beta strandi1386 – 1393Combined sources8
Helixi1397 – 1409Combined sources13
Beta strandi1414 – 1417Combined sources4
Helixi1423 – 1425Combined sources3
Beta strandi1428 – 1436Combined sources9
Beta strandi1442 – 1444Combined sources3
Beta strandi1449 – 1453Combined sources5
Beta strandi1456 – 1463Combined sources8
Beta strandi1467 – 1469Combined sources3
Beta strandi1471 – 1478Combined sources8
Helixi1481 – 1488Combined sources8
Beta strandi1493 – 1495Combined sources3
Beta strandi1497 – 1502Combined sources6
Helixi1514 – 1527Combined sources14
Helixi1532 – 1544Combined sources13
Beta strandi1545 – 1548Combined sources4
Helixi1555 – 1564Combined sources10
Helixi1570 – 1578Combined sources9
Helixi1584 – 1597Combined sources14
Helixi1606 – 1611Combined sources6
Turni1614 – 1618Combined sources5
Beta strandi1627 – 1629Combined sources3
Beta strandi1635 – 1637Combined sources3
Helixi1640 – 1652Combined sources13
Beta strandi1680 – 1687Combined sources8
Helixi1753 – 1777Combined sources25
Helixi1940 – 1964Combined sources25
Helixi1976 – 1999Combined sources24
Beta strandi2422 – 2426Combined sources5
Helixi2445 – 2450Combined sources6
Helixi2454 – 2456Combined sources3
Beta strandi2457 – 2459Combined sources3
Helixi2462 – 2464Combined sources3
Helixi2465 – 2472Combined sources8
Helixi2482 – 2495Combined sources14
Helixi2505 – 2510Combined sources6
Helixi2525 – 2529Combined sources5
Helixi2533 – 2548Combined sources16
Beta strandi2550 – 2552Combined sources3
Beta strandi2556 – 2560Combined sources5
Beta strandi2564 – 2566Combined sources3
Helixi2569 – 2571Combined sources3
Beta strandi2579 – 2582Combined sources4
Helixi2585 – 2607Combined sources23
Helixi2608 – 2610Combined sources3
Helixi2612 – 2614Combined sources3
Helixi2617 – 2629Combined sources13
Beta strandi2631 – 2639Combined sources9
Helixi2644 – 2647Combined sources4
Helixi2650 – 2660Combined sources11
Helixi2667 – 2679Combined sources13
Turni2680 – 2682Combined sources3
Beta strandi2684 – 2687Combined sources4
Beta strandi2693 – 2697Combined sources5
Helixi2707 – 2726Combined sources20
Beta strandi2729 – 2736Combined sources8
Beta strandi2739 – 2745Combined sources7
Helixi2749 – 2765Combined sources17
Beta strandi2770 – 2772Combined sources3
Helixi2780 – 2782Combined sources3
Beta strandi2788 – 2794Combined sources7
Beta strandi2800 – 2806Combined sources7
Helixi2809 – 2820Combined sources12
Helixi2827 – 2835Combined sources9
Helixi2839 – 2843Combined sources5
Helixi2845 – 2855Combined sources11
Beta strandi2863 – 2867Combined sources5
Beta strandi2870 – 2874Combined sources5
Helixi2876 – 2878Combined sources3
Helixi2879 – 2887Combined sources9
Helixi2889 – 2892Combined sources4
Helixi2899 – 2912Combined sources14
Helixi2917 – 2934Combined sources18
Helixi2936 – 2945Combined sources10
Helixi2947 – 2949Combined sources3
Beta strandi2950 – 2952Combined sources3
Helixi2960 – 2964Combined sources5
Turni2968 – 2971Combined sources4
Beta strandi2984 – 2986Combined sources3
Helixi2994 – 3007Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A1RX-ray2.50A/B1027-1206[»]
1A1VX-ray2.20A1193-1657[»]
1CWXNMR-A2-45[»]
1HEIX-ray2.10A/B1206-1656[»]
1JR6NMR-A1353-1456[»]
A1478-1507[»]
1N1LX-ray2.60A/B1027-1206[»]
1ONBNMR-A1353-1456[»]
A1478-1507[»]
1R7CNMR-A1973-2003[»]
1R7DNMR-A1973-2003[»]
1R7ENMR-A1973-2003[»]
1R7FNMR-A1973-2003[»]
1R7GNMR-A1973-2003[»]
1RGQX-ray2.90A/B1027-1207[»]
2A4RX-ray2.40A/C1027-1207[»]
B/D1680-1696[»]
2F9VX-ray2.60A/C1027-1207[»]
B/D1678-1696[»]
2HD0X-ray2.28A/B/C/D/E/F/G/H/I/J/K/L903-1026[»]
2JXFNMR-A1751-1780[»]
2KDRNMR-X1938-1965[»]
2N1PNMR-A2982-3011[»]
2O8MX-ray2.00A/B1027-1207[»]
C/D1678-1696[»]
2OBOX-ray2.60A/C1022-1207[»]
B/D1677-1695[»]
2OBQX-ray2.50A/C1027-1207[»]
B/D1678-1696[»]
2OC0X-ray2.30A/C1027-1207[»]
B/D1680-1696[»]
2OC1X-ray2.70A/C1027-1207[»]
B/D1680-1696[»]
2OC7X-ray2.70A/C1027-1207[»]
B/D1680-1696[»]
2OC8X-ray2.66A/C1027-1207[»]
B/D1680-1696[»]
2OINX-ray2.50A/B1027-1207[»]
C/D1678-1696[»]
2P59X-ray2.90C/D1678-1696[»]
2QV1X-ray2.40C/D1678-1696[»]
2XI2X-ray1.80A/B/C2421-2990[»]
2XI3X-ray1.70A/B2421-2990[»]
2XNIX-ray3.30A/B1027-1206[»]
4CL1X-ray3.50A/B/C/D2005-2174[»]
4JZNX-ray2.05K434-446[»]
4JZOX-ray2.22I/J/K/L434-446[»]
4MWFX-ray2.64C/D412-459[»]
C/D486-645[»]
4N0YX-ray1.75A314-324[»]
4Q0XX-ray2.90E421-446[»]
4XVJX-ray2.00A412-423[»]
4Z0XX-ray2.00C435-446[»]
5EOCX-ray1.98P/Q412-422[»]
5FGBX-ray1.65F/G405-425[»]
5FGCX-ray1.90A405-425[»]
DisProtiDP00588.
ProteinModelPortaliP27958.
SMRiP27958.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP27958.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini899 – 1026Peptidase C18PROSITE-ProRule annotationAdd BLAST128
Domaini1217 – 1369Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST153
Domaini2634 – 2752RdRp catalyticPROSITE-ProRule annotationAdd BLAST119

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 59Interaction with DDX3XBy similarityAdd BLAST58
Regioni2 – 23Interaction with STAT1By similarityAdd BLAST22
Regioni122 – 173Interaction with APOA2By similarityAdd BLAST52
Regioni150 – 159Mitochondrial targeting signalBy similarity10
Regioni164 – 167Important for lipid droplets localizationBy similarity4
Regioni265 – 296Fusion peptideSequence analysisAdd BLAST32
Regioni385 – 411HVR1By similarityAdd BLAST27
Regioni475 – 481HVR2By similarity7
Regioni482 – 494CD81-binding 1Sequence analysisAdd BLAST13
Regioni522 – 553CD81-binding 2Sequence analysisAdd BLAST32
Regioni660 – 671PKR/eIF2-alpha phosphorylation homology domain (PePHD)Add BLAST12
Regioni1679 – 1690NS3-binding (by NS4A)Sequence analysisAdd BLAST12
Regioni2120 – 2332Transcriptional activationSequence analysisAdd BLAST213
Regioni2120 – 2208FKBP8-bindingSequence analysisAdd BLAST89
Regioni2200 – 2250Basal phosphorylationBy similarityAdd BLAST51
Regioni2210 – 2275PKR-bindingSequence analysisAdd BLAST66
Regioni2249 – 2306NS4B-bindingSequence analysisAdd BLAST58
Regioni2351 – 2420Basal phosphorylationBy similarityAdd BLAST70
Regioni2354 – 2377V3Add BLAST24

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi5 – 13Nuclear localization signalSequence analysis9
Motifi38 – 43Nuclear localization signalSequence analysis6
Motifi58 – 64Nuclear localization signalSequence analysis7
Motifi66 – 71Nuclear localization signalSequence analysis6
Motifi1316 – 1319DECH box4
Motifi2322 – 2325SH3-bindingSequence analysis4
Motifi2327 – 2335Nuclear localization signalSequence analysis9

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi796 – 803Poly-Leu8
Compositional biasi1432 – 1435Poly-Val4
Compositional biasi2286 – 2327Pro-richAdd BLAST42
Compositional biasi2996 – 2999Poly-Leu4

Domaini

The transmembrane regions of envelope E1 and E2 glycoproteins are involved in heterodimer formation, ER localization, and assembly of these proteins. Envelope E2 glycoprotein contain two highly variable regions called hypervariable region 1 and 2 (HVR1 and HVR2). E2 also contain two segments involved in CD81-binding. HVR1 is implicated in the SCARB1-mediated cell entry. HVR2 and CD81-binding regions may be involved in sensitivity and/or resistance to IFN-alpha therapy (By similarity).By similarity
The N-terminus of NS5A acts as membrane anchor. The central part of NS5A seems to be intrinsically disordered and interacts with NS5B and host PKR. The C-terminus of NS5A contains a variable region called variable region 3 (V3) (By similarity).By similarity
The SH3-binding domain of NS5A is involved in the interaction with human Bin1, GRB2 and Src-family kinases.By similarity
The N-terminal one-third of serine protease NS3 contains the protease activity. This region contains a zinc atom that does not belong to the active site, but may play a structural rather than a catalytic role. This region is essential for the activity of protease NS2-3, maybe by contributing to the folding of the latter. The helicase activity is located in the C-terminus of NS3.1 Publication

Sequence similaritiesi

Belongs to the hepacivirus polyprotein family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 peptidase C18 domain.PROSITE-ProRule annotation
Contains 1 peptidase S29 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Keywords - Domaini

SH3-binding, Transmembrane, Transmembrane helix

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011492. DEAD_Flavivir.
IPR002521. HCV_core_C.
IPR002522. HCV_core_N.
IPR002519. HCV_env.
IPR002531. HCV_NS1.
IPR002518. HCV_NS2.
IPR000745. HCV_NS4a.
IPR001490. HCV_NS4b.
IPR002868. HCV_NS5a.
IPR013193. HCV_NS5a_1B_dom.
IPR024350. HCV_NS5a_C.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR013192. NS5A_1a.
IPR027417. P-loop_NTPase.
IPR009003. Peptidase_S1_PA.
IPR004109. Peptidase_S29.
IPR007094. RNA-dir_pol_PSvirus.
IPR002166. RNA_pol_HCV.
[Graphical view]
PfamiPF07652. Flavi_DEAD. 1 hit.
PF01543. HCV_capsid. 1 hit.
PF01542. HCV_core. 1 hit.
PF01539. HCV_env. 1 hit.
PF01560. HCV_NS1. 1 hit.
PF01538. HCV_NS2. 1 hit.
PF01006. HCV_NS4a. 1 hit.
PF01001. HCV_NS4b. 1 hit.
PF01506. HCV_NS5a. 1 hit.
PF08300. HCV_NS5a_1a. 1 hit.
PF08301. HCV_NS5a_1b. 1 hit.
PF12941. HCV_NS5a_C. 1 hit.
PF02907. Peptidase_S29. 1 hit.
PF00998. RdRP_3. 1 hit.
[Graphical view]
ProDomiPD001388. HCV_env. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51693. HCV_NS2_PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Note: The exact location of the ribosomal frameshift is unknown. The F protein seems to be generated by a -2 ribosomal frameshift located in the vicinity of codon 11 of the core protein coding sequence. However, some F proteins may also be generated by +1 ribosomal frameshift. Since the core gene encodes alternative reading frame proteins (ARFPs), many functions depicted for the core protein might belong to the ARFPs.
Isoform Genome polyprotein (identifier: P27958-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSTNPKPQRK TKRNTNRRPQ DVKFPGGGQI VGGVYLLPRR GPRLGVRATR
60 70 80 90 100
KTSERSQPRG RRQPIPKARR PEGRTWAQPG YPWPLYGNEG CGWAGWLLSP
110 120 130 140 150
RGSRPSWGPT DPRRRSRNLG KVIDTLTCGF ADLMGYIPLV GAPLGGAARA
160 170 180 190 200
LAHGVRVLED GVNYATGNLP GCSFSIFLLA LLSCLTVPAS AYQVRNSSGL
210 220 230 240 250
YHVTNDCPNS SVVYEAADAI LHTPGCVPCV REGNASRCWV AVTPTVATRD
260 270 280 290 300
GKLPTTQLRR HIDLLVGSAT LCSALYVGDL CGSVFLVGQL FTFSPRHHWT
310 320 330 340 350
TQDCNCSIYP GHITGHRMAW NMMMNWSPTA ALVVAQLLRI PQAIMDMIAG
360 370 380 390 400
AHWGVLAGIK YFSMVGNWAK VLVVLLLFAG VDAETHVTGG NAGRTTAGLV
410 420 430 440 450
GLLTPGAKQN IQLINTNGSW HINSTALNCN ESLNTGWLAG LFYQHKFNSS
460 470 480 490 500
GCPERLASCR RLTDFAQGWG PISYANGSGL DERPYCWHYP PRPCGIVPAK
510 520 530 540 550
SVCGPVYCFT PSPVVVGTTD RSGAPTYSWG ANDTDVFVLN NTRPPLGNWF
560 570 580 590 600
GCTWMNSTGF TKVCGAPPCV IGGVGNNTLL CPTDCFRKYP EATYSRCGSG
610 620 630 640 650
PRITPRCMVD YPYRLWHYPC TINYTIFKVR MYVGGVEHRL EAACNWTRGE
660 670 680 690 700
RCDLEDRDRS ELSPLLLSTT QWQVLPCSFT TLPALSTGLI HLHQNIVDVQ
710 720 730 740 750
YLYGVGSSIA SWAIKWEYVV LLFLLLADAR VCSCLWMMLL ISQAEAALEN
760 770 780 790 800
LVILNAASLA GTHGLVSFLV FFCFAWYLKG RWVPGAVYAL YGMWPLLLLL
810 820 830 840 850
LALPQRAYAL DTEVAASCGG VVLVGLMALT LSPYYKRYIS WCMWWLQYFL
860 870 880 890 900
TRVEAQLHVW VPPLNVRGGR DAVILLTCVV HPALVFDITK LLLAIFGPLW
910 920 930 940 950
ILQASLLKVP YFVRVQGLLR ICALARKIAG GHYVQMAIIK LGALTGTCVY
960 970 980 990 1000
NHLAPLRDWA HNGLRDLAVA VEPVVFSRME TKLITWGADT AACGDIINGL
1010 1020 1030 1040 1050
PVSARRGQEI LLGPADGMVS KGWRLLAPIT AYAQQTRGLL GCIITSLTGR
1060 1070 1080 1090 1100
DKNQVEGEVQ IVSTATQTFL ATCINGVCWT VYHGAGTRTI ASPKGPVIQT
1110 1120 1130 1140 1150
YTNVDQDLVG WPAPQGSRSL TPCTCGSSDL YLVTRHADVI PVRRRGDSRG
1160 1170 1180 1190 1200
SLLSPRPISY LKGSSGGPLL CPTGHAVGLF RAAVCTRGVA KAVDFIPVEN
1210 1220 1230 1240 1250
LETTMRSPVF TDNSSPPAVP QSFQVAHLHA PTGSGKSTKV PAAYAAKGYK
1260 1270 1280 1290 1300
VLVLNPSVAA TLGFGAYMSK AHGVDPNIRT GVRTITTGSP ITYSTYGKFL
1310 1320 1330 1340 1350
ADAGCSGGAY DIIICDECHS TDATSISGIG TVLDQAETAG ARLVVLATAT
1360 1370 1380 1390 1400
PPGSVTVSHP NIEEVALSTT GEIPFYGKAI PLEVIKGGRH LIFCHSKKKC
1410 1420 1430 1440 1450
DELAAKLVAL GINAVAYYRG LDVSVIPTSG DVVVVSTDAL MTGFTGDFDS
1460 1470 1480 1490 1500
VIDCNTCVTQ TVDFSLDPTF TIETTTLPQD AVSRTQRRGR TGRGKPGIYR
1510 1520 1530 1540 1550
FVAPGERPSG MFDSSVLCEC YDAGCAWYEL TPAETTVRLR AYMNTPGLPV
1560 1570 1580 1590 1600
CQDHLGFWEG VFTGLTHIDA HFLSQTKQSG ENFPYLVAYQ ATVCARAQAP
1610 1620 1630 1640 1650
PPSWDQMRKC LIRLKPTLHG PTPLLYRLGA VQNEVTLTHP ITKYIMTCMS
1660 1670 1680 1690 1700
ADLEVVTSTW VLVGGVLAAL AAYCLSTGCV VIVGRIVLSG KPAIIPDREV
1710 1720 1730 1740 1750
LYQEFDEMEE CSQHLPYIEQ GMMLAEQFKQ KALGLLQTAS RHAEVITPAV
1760 1770 1780 1790 1800
QTNWQKLEVF WAKHMWNFIS GIQYLAGLST LPGNPAIASL MAFTAAVTSP
1810 1820 1830 1840 1850
LTTGQTLLFN ILGGWVAAQL AAPGAATAFV GAGLAGAALD SVGLGKVLVD
1860 1870 1880 1890 1900
ILAGYGAGVA GALVAFKIMS GEVPSTEDLV NLLPAILSPG ALAVGVVFAS
1910 1920 1930 1940 1950
ILRRRVGPGE GAVQWMNRLI AFASRGNHVS PTHYVPESDA AARVTAILSS
1960 1970 1980 1990 2000
LTVTQLLRRL HQWISSECTT PCSGSWLRDI WDWICEVLSD FKTWLKAKLM
2010 2020 2030 2040 2050
PQLPGIPFVS CQRGYRGVWR GDGIMHTRCH CGAEITGHVK NGTMRIVGPR
2060 2070 2080 2090 2100
TCKNMWSGTF FINAYTTGPC TPLPAPNYKF ALWRVSAEEY VEIRRVGDFH
2110 2120 2130 2140 2150
YVSGMTTDNL KCPCQIPSPE FFTELDGVRL HRFAPPCKPL LREEVSFRVG
2160 2170 2180 2190 2200
LHEYPVGSQL PCEPEPDVAV LTSMLTDPSH ITAEAAGRRL ARGSPPSMAS
2210 2220 2230 2240 2250
SSASQLSAPS LKATCTANHD SPDAELIEAN LLWRQEMGGN ITRVESENKV
2260 2270 2280 2290 2300
VILDSFDPLV AEEDEREVSV PAEILRKSRR FAPALPVWAR PDYNPLLVET
2310 2320 2330 2340 2350
WKKPDYEPPV VHGCPLPPPR SPPVPPPRKK RTVVLTESTL PTALAELATK
2360 2370 2380 2390 2400
SFGSSSTSGI TGDNTTTSSE PAPSGCPPDS DVESYSSMPP LEGEPGDPDL
2410 2420 2430 2440 2450
SDGSWSTVSS GADTEDVVCC SMSYSWTGAL VTPCAAEEQK LPINALSNSL
2460 2470 2480 2490 2500
LRHHNLVYST TSRSACQRKK KVTFDRLQVL DSHYQDVLKE VKAAASKVKA
2510 2520 2530 2540 2550
NLLSVEEACS LAPPHSAKSK FGYGAKDVRC HARKAVAHIN SVWKDLLEDS
2560 2570 2580 2590 2600
VTPIDTTIMA KNEVFCVQPE KGGRKPARLI VFPDLGVRVC EKMALYDVVS
2610 2620 2630 2640 2650
KLPLAVMGSS YGFQYSPGQR VEFLVQAWKS KKTPMGLSYD TRCFDSTVTE
2660 2670 2680 2690 2700
SDIRTEEAIY QCCDLDPQAR VAIKSLTERL YVGGPLTNSR GENCGYRRCR
2710 2720 2730 2740 2750
ASRVLTTSCG NTLTRYIKAR AACRAAGLQD CTMLVCGDDL VVICESAGVQ
2760 2770 2780 2790 2800
EDAASLRAFT EAMTRYSAPP GDPPQPEYDL ELITSCSSNV SVAHDGAGKR
2810 2820 2830 2840 2850
VYYLTRDPTT PLARAAWETA RHTPVNSWLG NIIMFAPTLW ARMILMTHFF
2860 2870 2880 2890 2900
SVLIARDQLE QALNCEIYGA CYSIEPLDLP PIIQRLHGLS AFSLHSYSPG
2910 2920 2930 2940 2950
EINRVAACLR KLGVPPLRAW RHRAWSVRAR LLARGGKAAI CGKYLFNWAV
2960 2970 2980 2990 3000
RTKLKLTPIT AAGRLDLSGW FTAGYSGGDI YHSVSHARPR WFWFCLLLLA
3010
AGVGIYLLPN R
Note: Produced by conventional translation.
Length:3,011
Mass (Da):327,146
Last modified:January 23, 2007 - v3
Checksum:i772CBB29CCD94753
GO
Isoform F protein (identifier: P0C045-1) [UniParc]FASTAAdd to basket
Also known as: Frameshifted protein
The sequence of this isoform can be found in the external entry P0C045.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by ribosomal frameshifting.
Length:162
Mass (Da):17,006
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti212V → I in strain: Isolate H77. 1
Natural varianti297H → R in strain: Isolate H77. 1
Natural varianti303D → S in strain: Isolate H77. 1
Natural varianti321N → D in strain: Isolate H77. 1
Natural varianti360K → A in strain: Isolate H77. 1
Natural varianti391N → S in strain: Isolate H77. 1
Natural varianti394R → H in strain: Isolate H77. 1
Natural varianti431E → D in strain: Isolate H77. 1
Natural varianti434N → T in strain: Isolate H77. 1
Natural varianti444Q → R in strain: Isolate H77. 1
Natural varianti457A → T in strain: Isolate H77. 1
Natural varianti564 – 566CGA → RGV in strain: Isolate H77. 3
Natural varianti589Y → H in strain: Isolate H77. 1
Natural varianti602R → W in strain: Isolate H77. 1
Natural varianti650E → G in strain: Isolate H77. 1
Natural varianti773C → R in strain: Isolate H77. 1
Natural varianti787V → A in strain: Isolate H77. 1
Natural varianti790L → F in strain: Isolate H77. 1
Natural varianti877T → M in strain: Isolate H77. 1
Natural varianti883A → T in strain: Isolate H77. 1
Natural varianti948C → Y in strain: Isolate H77. 1
Natural varianti954A → T in strain: Isolate H77. 1
Natural varianti1026L → Q in strain: Isolate H77. 1
Natural varianti1033A → T in strain: Isolate H77. 1
Natural varianti1049G → S in strain: Isolate H77. 1
Natural varianti1100T → M in strain: Isolate H77. 1
Natural varianti1121T → A in strain: Isolate H77. 1
Natural varianti1173T → A in strain: Isolate H77. 1
Natural varianti1202E → G in strain: Isolate H77. 1
Natural varianti1214S → P in strain: Isolate H77. 1
Natural varianti1247K → Q in strain: Isolate H77. 1
Natural varianti1303A → G in strain: Isolate H77. 1
Natural varianti1327S → L in strain: Isolate H77. 1
Natural varianti1556G → E in strain: Isolate H77. 1
Natural varianti1608R → W in strain: Isolate H77. 1
Natural varianti1742H → Q in strain: Isolate H77. 1
Natural varianti1839 – 1840LD → IG in strain: Isolate H77. 2
Natural varianti1893A → V in strain: Isolate H77. 1
Natural varianti1898 – 1900FAS → CAA in strain: Isolate H77. 3
Natural varianti1905R → H in strain: Isolate H77. 1
Natural varianti1940A → V in strain: Isolate H77. 1
Natural varianti2043T → A in strain: Isolate H77. 1
Natural varianti2053K → R in strain: Isolate H77. 1
Natural varianti2061F → L in strain: Isolate H77. 1
Natural varianti2102V → I in strain: Isolate H77. 1
Natural varianti2185A → E in strain: Isolate H77. 1
Natural varianti2283P → R in strain: Isolate H77. 1
Natural varianti2296L → P in strain: Isolate H77. 1
Natural varianti2341P → S in strain: Isolate H77. 1
Natural varianti2355S → P in strain: Isolate H77. 1
Natural varianti2400L → F in strain: Isolate H77. 1
Natural varianti2425S → T in strain: Isolate H77. 1
Natural varianti2469K → Q in strain: Isolate H77. 1
Natural varianti2512A → T in strain: Isolate H77. 1
Natural varianti2637L → F in strain: Isolate H77. 1
Natural varianti2703R → G in strain: Isolate H77. 1
Natural varianti2715R → C in strain: Isolate H77. 1
Natural varianti2755S → N in strain: Isolate H77. 1
Natural varianti2925W → R in strain: Isolate H77. 1
Natural varianti2933A → S in strain: Isolate H77. 1
Natural varianti2937K → R in strain: Isolate H77. 1
Natural varianti2960T → A in strain: Isolate H77. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M67463 Genomic RNA. Translation: AAA45534.1.
AF009606 Genomic RNA. Translation: AAB66324.1.
AF011751 Genomic RNA. Translation: AAB67036.1.
AF011752 Genomic RNA. Translation: AAB67037.1.
AF011753 Genomic RNA. Translation: AAB67038.1.
PIRiA36814. GNWVCH.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Web resourcesi

euHCVdb

The European HCV database

Virus Pathogen Resource

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M67463 Genomic RNA. Translation: AAA45534.1.
AF009606 Genomic RNA. Translation: AAB66324.1.
AF011751 Genomic RNA. Translation: AAB67036.1.
AF011752 Genomic RNA. Translation: AAB67037.1.
AF011753 Genomic RNA. Translation: AAB67038.1.
PIRiA36814. GNWVCH.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A1RX-ray2.50A/B1027-1206[»]
1A1VX-ray2.20A1193-1657[»]
1CWXNMR-A2-45[»]
1HEIX-ray2.10A/B1206-1656[»]
1JR6NMR-A1353-1456[»]
A1478-1507[»]
1N1LX-ray2.60A/B1027-1206[»]
1ONBNMR-A1353-1456[»]
A1478-1507[»]
1R7CNMR-A1973-2003[»]
1R7DNMR-A1973-2003[»]
1R7ENMR-A1973-2003[»]
1R7FNMR-A1973-2003[»]
1R7GNMR-A1973-2003[»]
1RGQX-ray2.90A/B1027-1207[»]
2A4RX-ray2.40A/C1027-1207[»]
B/D1680-1696[»]
2F9VX-ray2.60A/C1027-1207[»]
B/D1678-1696[»]
2HD0X-ray2.28A/B/C/D/E/F/G/H/I/J/K/L903-1026[»]
2JXFNMR-A1751-1780[»]
2KDRNMR-X1938-1965[»]
2N1PNMR-A2982-3011[»]
2O8MX-ray2.00A/B1027-1207[»]
C/D1678-1696[»]
2OBOX-ray2.60A/C1022-1207[»]
B/D1677-1695[»]
2OBQX-ray2.50A/C1027-1207[»]
B/D1678-1696[»]
2OC0X-ray2.30A/C1027-1207[»]
B/D1680-1696[»]
2OC1X-ray2.70A/C1027-1207[»]
B/D1680-1696[»]
2OC7X-ray2.70A/C1027-1207[»]
B/D1680-1696[»]
2OC8X-ray2.66A/C1027-1207[»]
B/D1680-1696[»]
2OINX-ray2.50A/B1027-1207[»]
C/D1678-1696[»]
2P59X-ray2.90C/D1678-1696[»]
2QV1X-ray2.40C/D1678-1696[»]
2XI2X-ray1.80A/B/C2421-2990[»]
2XI3X-ray1.70A/B2421-2990[»]
2XNIX-ray3.30A/B1027-1206[»]
4CL1X-ray3.50A/B/C/D2005-2174[»]
4JZNX-ray2.05K434-446[»]
4JZOX-ray2.22I/J/K/L434-446[»]
4MWFX-ray2.64C/D412-459[»]
C/D486-645[»]
4N0YX-ray1.75A314-324[»]
4Q0XX-ray2.90E421-446[»]
4XVJX-ray2.00A412-423[»]
4Z0XX-ray2.00C435-446[»]
5EOCX-ray1.98P/Q412-422[»]
5FGBX-ray1.65F/G405-425[»]
5FGCX-ray1.90A405-425[»]
DisProtiDP00588.
ProteinModelPortaliP27958.
SMRiP27958.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP27958. 231 interactors.
MINTiMINT-106294.

Chemistry databases

BindingDBiP27958.
ChEMBLiCHEMBL3638344.

PTM databases

iPTMnetiP27958.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

euHCVdbiAF009606.
AF011751.
AF011752.
AF011753.
M67463.

Enzyme and pathway databases

BRENDAi3.4.21.98. 2642.
3.6.4.13. 2642.

Miscellaneous databases

EvolutionaryTraceiP27958.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011492. DEAD_Flavivir.
IPR002521. HCV_core_C.
IPR002522. HCV_core_N.
IPR002519. HCV_env.
IPR002531. HCV_NS1.
IPR002518. HCV_NS2.
IPR000745. HCV_NS4a.
IPR001490. HCV_NS4b.
IPR002868. HCV_NS5a.
IPR013193. HCV_NS5a_1B_dom.
IPR024350. HCV_NS5a_C.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR013192. NS5A_1a.
IPR027417. P-loop_NTPase.
IPR009003. Peptidase_S1_PA.
IPR004109. Peptidase_S29.
IPR007094. RNA-dir_pol_PSvirus.
IPR002166. RNA_pol_HCV.
[Graphical view]
PfamiPF07652. Flavi_DEAD. 1 hit.
PF01543. HCV_capsid. 1 hit.
PF01542. HCV_core. 1 hit.
PF01539. HCV_env. 1 hit.
PF01560. HCV_NS1. 1 hit.
PF01538. HCV_NS2. 1 hit.
PF01006. HCV_NS4a. 1 hit.
PF01001. HCV_NS4b. 1 hit.
PF01506. HCV_NS5a. 1 hit.
PF08300. HCV_NS5a_1a. 1 hit.
PF08301. HCV_NS5a_1b. 1 hit.
PF12941. HCV_NS5a_C. 1 hit.
PF02907. Peptidase_S29. 1 hit.
PF00998. RdRP_3. 1 hit.
[Graphical view]
ProDomiPD001388. HCV_env. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51693. HCV_NS2_PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_HCVH
AccessioniPrimary (citable) accession number: P27958
Secondary accession number(s): O36579
, O36608, O36609, O36610
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 193 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Cell culture adaptation of the virus leads to mutations in NS5A, reducing its inhibitory effect on replication.By similarity
Core protein exerts viral interference on hepatitis B virus when HCV and HBV coinfect the same cell, by suppressing HBV gene expression, RNA encapsidation and budding.By similarity

Caution

The core gene probably also codes for alternative reading frame proteins (ARFPs). Many functions depicted for the core protein might belong to the ARFPs.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.