O39927 (POLG_HCVEU) Reviewed, UniProtKB/Swiss-Prot
Last modified October 16, 2013. Version 109. History...
Names and origin
|Protein names||Recommended name:|
Cleaved into the following 11 chains:
|Organism||Hepatitis C virus genotype 6a (isolate EUHK2) (HCV) [Complete proteome]|
|Taxonomic identifier||356420 [NCBI]|
|Taxonomic lineage||Viruses › ssRNA positive-strand viruses, no DNA stage › Flaviviridae › Hepacivirus ›|
|Virus host||Homo sapiens (Human) [TaxID: 9606]|
|Sequence length||3018 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
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.
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.
P7 seems to be a heptameric ion channel protein (viroporin) and is inhibited by the antiviral drug amantadine. Also inhibited by long-alkyl-chain iminosugar derivatives. Essential for infectivity By similarity.
Protease NS2-3 is a cysteine protease responsible for the autocatalytic cleavage of NS2-NS3. Seems to undergo self-inactivation following maturation 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. Cleaves and inhibits the host antiviral protein MAVS By similarity.
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 By similarity.
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.
NS5B is a RNA-dependent RNA polymerase that plays an essential role in the virus replication By similarity.
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).
NTP + H2O = NDP + phosphate.
ATP + H2O = ADP + phosphate.
Binds 1 zinc ion per NS3 protease domain By similarity.
Binds 1 zinc ion per NS5A N-terminal domain By similarity.
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.
Core protein is a homomultimer that binds the C-terminal part of E1 and interacts with numerous cellular proteins. 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). 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. Ref.4
Core protein p21: Host endoplasmic reticulum membrane; Single-pass membrane protein By similarity. Host mitochondrion membrane; Single-pass type I membrane protein By similarity. Host lipid droplet By similarity. Note: The C-terminal transmembrane domain of core protein p21 contains an ER signal leading the nascent polyprotein to the ER membrane. Only a minor proportion of core protein is present in the nucleus and an unknown proportion is secreted. Ref.3
Envelope glycoprotein E1: Virion membrane; Single-pass type I membrane protein Potential. Host endoplasmic reticulum membrane; Single-pass type I membrane protein By similarity. 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. Ref.3
Envelope glycoprotein E2: Virion membrane; Single-pass type I membrane protein Potential. Host endoplasmic reticulum membrane; Single-pass type I membrane protein By similarity. 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. Ref.3
p7: Host endoplasmic reticulum membrane; Multi-pass membrane protein By similarity Ref.3. Host cell membrane By similarity. Note: The C-terminus of p7 membrane domain acts as a signal sequence. After cleavage by host signal peptidase, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor. Only a fraction localizes to the plasma membrane. Ref.3
Non-structural protein 5A: Host endoplasmic reticulum membrane; Peripheral membrane protein By similarity. Host cytoplasm › host perinuclear region By similarity. Host mitochondrion By similarity. Note: Host membrane insertion occurs after processing by the NS3 protease. Ref.3
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 a highly variable region called hypervariable region 1 (HVR1). E2 also contains two segments involved in CD81-binding. HVR1 is implicated in the SCARB1-mediated cell entry. CD81-binding regions may be involved in sensitivity and/or resistance to IFN-alpha therapy By similarity.
The N-terminus of NS5A act as membrane anchor. The central part of NS5A seems to be intrinsically disordered and interacts with NS5B and host PKR 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 By similarity.
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.
Envelope E1 and E2 glycoproteins are highly N-glycosylated By similarity.
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.
NS4B is palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions 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.
Core protein is ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation By similarity.
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.
Belongs to the hepacivirus polyprotein family.
Contains 1 peptidase C18 domain.
Contains 1 peptidase S29 domain.
Contains 1 RdRp catalytic domain.
The core gene probably also codes for alternative reading frame proteins (ARFPs). Many functions depicted for the core protein might belong to the ARFPs.
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Initiator methionine||1||1||Removed; by host By similarity|
|Chain||2 – 191||190||Core protein p21 Potential||PRO_0000045544|
|Chain||2 – 177||176||Core protein p19 By similarity||PRO_0000045545|
|Propeptide||178 – 191||14||ER anchor for the core protein, removed in mature form by host signal peptidase By similarity||PRO_0000045546|
|Chain||192 – 383||192||Envelope glycoprotein E1 Potential||PRO_0000045547|
|Chain||384 – 750||367||Envelope glycoprotein E2 Potential||PRO_0000045548|
|Chain||751 – 813||63||p7 By similarity||PRO_0000045549|
|Chain||814 – 1030||217||Protease NS2-3 Potential||PRO_0000045550|
|Chain||1031 – 1661||631||Serine protease NS3 Potential||PRO_0000045551|
|Chain||1662 – 1715||54||Non-structural protein 4A Potential||PRO_0000045552|
|Chain||1716 – 1976||261||Non-structural protein 4B Potential||PRO_0000045553|
|Chain||1977 – 2427||451||Non-structural protein 5A Potential||PRO_0000045554|
|Chain||2428 – 3018||591||RNA-directed RNA polymerase Potential||PRO_0000045555|
|Topological domain||2 – 168||167||Cytoplasmic Potential|
|Transmembrane||169 – 189||21||Helical; Potential|
|Topological domain||190 – 358||169||Lumenal Potential|
|Transmembrane||359 – 379||21||Helical; Potential|
|Topological domain||380 – 729||350||Lumenal Potential|
|Transmembrane||730 – 750||21||Helical; Potential|
|Topological domain||751 – 761||11||Lumenal Potential|
|Transmembrane||762 – 782||21||Helical; Potential|
|Topological domain||783 – 786||4||Cytoplasmic Potential|
|Transmembrane||787 – 807||21||Helical; Potential|
|Topological domain||808 – 817||10||Lumenal Potential|
|Transmembrane||818 – 838||21||Helical; Potential|
|Topological domain||839 – 885||47||Cytoplasmic Potential|
|Transmembrane||886 – 906||21||Helical; Potential|
|Topological domain||907 – 932||26||Lumenal Potential|
|Transmembrane||933 – 953||21||Helical; Potential|
|Topological domain||954 – 1661||708||Cytoplasmic Potential|
|Transmembrane||1662 – 1682||21||Helical; Potential|
|Topological domain||1683 – 1809||127||Cytoplasmic Potential|
|Transmembrane||1810 – 1830||21||Helical; Potential|
|Topological domain||1831 – 1832||2||Lumenal Potential|
|Transmembrane||1833 – 1853||21||Helical; Potential|
|Topological domain||1854||1||Cytoplasmic Potential|
|Transmembrane||1855 – 1875||21||Helical; Potential|
|Topological domain||1876 – 1885||10||Lumenal Potential|
|Transmembrane||1886 – 1906||21||Helical; Potential|
|Topological domain||1907 – 1976||70||Cytoplasmic Potential|
|Intramembrane||1977 – 2006||30||By similarity|
|Topological domain||2007 – 2997||991||Cytoplasmic Potential|
|Transmembrane||2998 – 3018||21||Helical; By similarity|
|Domain||2641 – 2759||119||RdRp catalytic|
|Nucleotide binding||1234 – 1241||8||ATP Potential|
|Region||2 – 59||58||Interaction with DDX3X By similarity|
|Region||2 – 23||22||Interaction with STAT1 By similarity|
|Region||122 – 173||52||Interaction with APOA2 By similarity|
|Region||150 – 159||10||Mitochondrial targeting signal By similarity|
|Region||164 – 167||4||Important for lipid droplets localization By similarity|
|Region||265 – 296||32||Fusion peptide Potential|
|Region||384 – 410||27||HVR1 By similarity|
|Region||482 – 494||13||CD81-binding 1 Potential|
|Region||522 – 553||32||CD81-binding 2 Potential|
|Region||664 – 675||12||PKR/eIF2-alpha phosphorylation homology domain (PePHD) By similarity|
|Region||1683 – 1694||12||NS3-binding (by NS4A) Potential|
|Region||2124 – 2337||214||Transcriptional activation Potential|
|Region||2124 – 2212||89||FKBP8-binding Potential|
|Region||2204 – 2254||51||Basal phosphorylation By similarity|
|Region||2214 – 2279||66||PKR-binding Potential|
|Region||2253 – 2311||59||NS4B-binding Potential|
|Region||2356 – 2427||72||Basal phosphorylation By similarity|
|Motif||5 – 13||9||Nuclear localization signal Potential|
|Motif||38 – 43||6||Nuclear localization signal Potential|
|Motif||58 – 64||7||Nuclear localization signal Potential|
|Motif||66 – 71||6||Nuclear localization signal Potential|
|Motif||1320 – 1323||4||DECH box By similarity|
|Motif||2327 – 2330||4||SH3-binding Potential|
|Motif||2332 – 2340||9||Nuclear localization signal Potential|
|Compositional bias||2282 – 2332||51||Pro-rich|
|Compositional bias||2999 – 3006||8||Poly-Leu|
|Active site||956||1||For protease NS2-3 activity; shared with dimeric partner By similarity|
|Active site||976||1||For protease NS2-3 activity; shared with dimeric partner By similarity|
|Active site||997||1||For protease NS2-3 activity; shared with dimeric partner By similarity|
|Active site||1087||1||Charge relay system; for serine protease NS3 activity By similarity|
|Active site||1111||1||Charge relay system; for serine protease NS3 activity By similarity|
|Active site||1169||1||Charge relay system; for serine protease NS3 activity By similarity|
|Metal binding||1127||1||Zinc By similarity|
|Metal binding||1129||1||Zinc By similarity|
|Metal binding||1175||1||Zinc By similarity|
|Metal binding||1179||1||Zinc By similarity|
|Metal binding||2015||1||Zinc By similarity|
|Metal binding||2033||1||Zinc By similarity|
|Metal binding||2035||1||Zinc By similarity|
|Metal binding||2056||1||Zinc By similarity|
|Site||177 – 178||2||Cleavage; by host signal peptidase By similarity|
|Site||191 – 192||2||Cleavage; by host signal peptidase Potential|
|Site||383 – 384||2||Cleavage; by host signal peptidase Potential|
|Site||750 – 751||2||Cleavage; by host signal peptidase By similarity|
|Site||813 – 814||2||Cleavage; by host signal peptidase By similarity|
|Site||1030 – 1031||2||Cleavage; by protease NS2-3 Potential|
|Site||1661 – 1662||2||Cleavage; by serine protease NS3 Potential|
|Site||1715 – 1716||2||Cleavage; by serine protease NS3 Potential|
|Site||1976 – 1977||2||Cleavage; by serine protease NS3 Potential|
|Site||2427 – 2428||2||Cleavage; by serine protease NS3 Potential|
Amino acid modifications
|Modified residue||2||1||N-acetylserine; by host By similarity|
|Modified residue||53||1||Phosphoserine; by host By similarity|
|Modified residue||99||1||Phosphoserine; by host By similarity|
|Modified residue||116||1||Phosphoserine; by host PKA By similarity|
|Modified residue||2198||1||Phosphoserine; by host; in p56 By similarity|
|Modified residue||2201||1||Phosphoserine; by host; in p58 By similarity|
|Modified residue||2205||1||Phosphoserine; by host; in p58 By similarity|
|Lipidation||1976||1||S-palmitoyl cysteine; by host By similarity|
|Glycosylation||196||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||209||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||234||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||250||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||305||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||416||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||422||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||429||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||447||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||475||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||532||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||556||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||577||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||627||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||649||1||N-linked (GlcNAc...); by host Potential|
|Glycosylation||712||1||N-linked (GlcNAc...); by host Potential|
|Disulfide bond||2118 ↔ 2166||By similarity|
|||"Complete coding sequence of hepatitis C virus genotype 6a."|
Adams A., Chamberlain R.W., Taylor L.A., Davidson F., Lin C.K., Simmonds P., Elliot R.M.
Biochem. Biophys. Res. Commun. 234:393-396(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
|||"Properties of the hepatitis C virus core protein: a structural protein that modulates cellular processes."|
J. Viral Hepat. 7:2-14(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
|||"Structural biology of hepatitis C virus."|
Penin F., Dubuisson J., Rey F.A., Moradpour D., Pawlotsky J.-M.
Hepatology 39:5-19(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW, SUBCELLULAR LOCATION.
|||"An RNA-binding protein, hnRNP A1, and a scaffold protein, septin 6, facilitate hepatitis C virus replication."|
Kim C.S., Seol S.K., Song O.-K., Park J.H., Jang S.K.
J. Virol. 81:3852-3865(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HNRNPA1 AND SEPT6.
|Y12083 Genomic RNA. Translation: CAA72801.1.|
3D structure databases
|SMR||O39927. Positions 2-45, 906-1030, 1033-1661, 1979-2007, 2012-2174, 2428-2990. |
Protein family/group databases
|TCDB||1.A.78.1.4. classical swine fever virus p7 viroporin (csfv-p7 viroporin) family. |
Protocols and materials databases
Family and domain databases
|InterPro||IPR011492. DEAD_Flavivir. |
|Pfam||PF07652. 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.
|ProDom||PD001388. HCV_env. 1 hit. |
[Graphical view] [Entries sharing at least one domain]
|SMART||SM00487. DEXDc. 1 hit. |
|SUPFAM||SSF50494. SSF50494. 1 hit. |
SSF52540. SSF52540. 2 hits.
|PROSITE||PS51192. HELICASE_ATP_BIND_1. 1 hit. |
PS51194. HELICASE_CTER. False negative.
PS50507. RDRP_SSRNA_POS. 1 hit.
|Accession||Primary (citable) accession number: O39927|
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Viral Protein Annotation Program|