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Q8JUX5

- POLS_CHIKS

UniProt

Q8JUX5 - POLS_CHIKS

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Protein
Structural polyprotein
Gene
N/A
Organism
Chikungunya virus (strain S27-African prototype) (CHIKV)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after endocytosis their membrane fuses with the target cell membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding By similarity.
E3 protein's function is unknown By similarity.
E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane By similarity.
6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins By similarity.
E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane By similarity.

Catalytic activityi

Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei139 – 1391Charge relay system By similarity
Active sitei145 – 1451Charge relay system By similarity
Active sitei213 – 2131Charge relay system By similarity
Sitei261 – 2622Cleavage; by capsid protein By similarity
Sitei325 – 3262Cleavage; by host furin By similarity
Sitei748 – 7492Cleavage; by host signal peptidase By similarity
Sitei809 – 8102Cleavage; by host signal peptidase By similarity

GO - Molecular functioni

  1. serine-type endopeptidase activity Source: InterPro
  2. structural molecule activity Source: InterPro

GO - Biological processi

  1. fusion of virus membrane with host endosome membrane Source: UniProtKB-KW
  2. virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Biological processi

Fusion of virus membrane with host endosomal membrane, Fusion of virus membrane with host membrane, Host-virus interaction, Viral attachment to host cell, Viral penetration into host cytoplasm, Virus entry into host cell

Protein family/group databases

MEROPSiS03.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyprotein
Alternative name(s):
p130
Cleaved into the following 6 chains:
Alternative name(s):
Coat protein
Short name:
C
Alternative name(s):
E3/E2
Alternative name(s):
Spike glycoprotein E3
Alternative name(s):
Spike glycoprotein E2
Alternative name(s):
Spike glycoprotein E1
OrganismiChikungunya virus (strain S27-African prototype) (CHIKV)
Taxonomic identifieri371094 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageTogaviridaeAlphavirusSFV complex
Virus hostiAedes aegypti (Yellowfever mosquito) (Culex aegypti) [TaxID: 7159]
Aedes albopictus (Asian tiger mosquito) (Stegomyia albopicta) [TaxID: 7160]
Aedes furcifer (Mosquito) [TaxID: 299627]
Aedes polynesiensis (Polynesian tiger mosquito) [TaxID: 188700]
Cercopithecus [TaxID: 9533]
Homo sapiens (Human) [TaxID: 9606]
Macaca (macaques) [TaxID: 9539]
Pan troglodytes (Chimpanzee) [TaxID: 9598]
Papio (baboons) [TaxID: 9554]
Presbytis [TaxID: 9573]
ProteomesiUP000000569: Genome

Subcellular locationi

Chain Capsid protein : Virion By similarity. Host cytoplasm By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini262 – 692431Extracellular Reviewed prediction
Add
BLAST
Transmembranei693 – 71321Helical; Reviewed prediction
Add
BLAST
Topological domaini714 – 74835Cytoplasmic Reviewed prediction
Add
BLAST
Topological domaini749 – 76315Extracellular Reviewed prediction
Add
BLAST
Transmembranei764 – 78421Helical; Reviewed prediction
Add
BLAST
Topological domaini785 – 79511Cytoplasmic Reviewed prediction
Add
BLAST
Transmembranei796 – 81621Helical; Reviewed prediction
Add
BLAST
Topological domaini817 – 1224408Extracellular Reviewed prediction
Add
BLAST
Transmembranei1225 – 124521Helical; Reviewed prediction
Add
BLAST
Topological domaini1246 – 12483Cytoplasmic Reviewed prediction

GO - Cellular componenti

  1. T=4 icosahedral viral capsid Source: UniProtKB-KW
  2. host cell cytoplasm Source: UniProtKB-SubCell
  3. host cell plasma membrane Source: UniProtKB-SubCell
  4. integral component of membrane Source: UniProtKB-KW
  5. virion membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host membrane, Membrane, T=4 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 261261Capsid protein By similarity
PRO_0000226219Add
BLAST
Chaini262 – 748487p62 By similarity
PRO_0000226220Add
BLAST
Chaini262 – 32564E3 protein By similarity
PRO_0000226221Add
BLAST
Signal peptidei262 – 27514Not cleaved Reviewed prediction
Add
BLAST
Chaini326 – 748423E2 envelope glycoprotein By similarity
PRO_0000226222Add
BLAST
Chaini749 – 809616K protein By similarity
PRO_0000226223Add
BLAST
Chaini810 – 1248439E1 envelope glycoprotein By similarity
PRO_0000226224Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi113 ↔ 128 By similarity
Glycosylationi273 – 2731N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi588 – 5881N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi670 – 6701N-linked (GlcNAc...); by host Reviewed prediction
Lipidationi721 – 7211S-palmitoyl cysteine; by host By similarity
Lipidationi741 – 7411S-palmitoyl cysteine; by host By similarity
Lipidationi742 – 7421S-palmitoyl cysteine; by host By similarity
Disulfide bondi858 ↔ 923 By similarity
Disulfide bondi871 ↔ 903 By similarity
Disulfide bondi872 ↔ 905 By similarity
Disulfide bondi877 ↔ 887 By similarity
Glycosylationi950 – 9501N-linked (GlcNAc...); by host Reviewed prediction
Disulfide bondi1068 ↔ 1080 By similarity
Disulfide bondi1110 ↔ 1185 By similarity
Disulfide bondi1115 ↔ 1189 By similarity
Disulfide bondi1137 ↔ 1179 By similarity
Lipidationi1242 – 12421S-stearoyl cysteine; by host By similarity

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. Capsid protein is auto-cleaved during polyprotein translation, unmasking p62 signal peptide. The remaining polyprotein is then targeted to the endoplasmic reticulum, where host signal peptidase cleaves it into p62, 6K and E1 proteins. p62 is further processed to mature E3 and E2 by host furin in trans-Golgi vesicle By similarity.
E2 is palmitoylated via thioester bonds. These palmitoylations may induce disruption of the C-terminus transmembrane. This would result in the reorientation of E2 c-terminus from lumenal to cytoplasmic side. 6K protein is also palmitoylated. E1 is stearoylated By similarity.

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Lipoprotein, Palmitate

Interactioni

Subunit structurei

p62 and E1 form a heterodimer shortly after synthesis. Processing of p62 into E2 and E3 results in a heterodimer of E2 and E1. Spike at virion surface are constituted of three E2-E1 heterodimers. After target cell attachment and endocytosis, E1 change conformation to form homotrimers By similarity.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi895 – 8995
Turni904 – 9074

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2RSWNMR-A893-910[»]
ProteinModelPortaliQ8JUX5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini113 – 261149Peptidase S3
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 107107Intrinsically disordered, in contact with genomic RNA in nucleocapsid Reviewed prediction
Add
BLAST
Regioni91 – 10010Ribosome-binding By similarity
Regioni721 – 74121Transient transmembrane before p62-6K protein processing Reviewed prediction
Add
BLAST
Regioni893 – 91018E1 fusion peptide loop By similarity
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi60 – 9839Lys-rich
Add
BLAST

Sequence similaritiesi

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Family and domain databases

Gene3Di2.60.40.350. 1 hit.
2.60.98.10. 3 hits.
InterProiIPR002548. Alpha_E1_glycop.
IPR000936. Alpha_E2_glycop.
IPR002533. Alpha_E3_glycop.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014756. Ig_E-set.
IPR000930. Peptidase_S3.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamiPF01589. Alpha_E1_glycop. 1 hit.
PF00943. Alpha_E2_glycop. 1 hit.
PF01563. Alpha_E3_glycop. 1 hit.
PF00944. Peptidase_S3. 1 hit.
[Graphical view]
PRINTSiPR00798. TOGAVIRIN.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF56983. SSF56983. 1 hit.
SSF81296. SSF81296. 1 hit.
PROSITEiPS51690. ALPHAVIRUS_CP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q8JUX5-1 [UniParc]FASTAAdd to Basket

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MEFIPTQTFY NRRYQPRPWT PRPTIQVIRP RPRPQRQAGQ LAQLISAVNK     50
LTMRAVPQQK PRRNRKNKKQ KQKQQAPQNN TNQKKQPPKK KPAQKKKKPG 100
RRERMCMKIE NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA 150
KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGGR 200
FTIPTGAGKP GDSGRPIFDN KGRVVAIVLG GANEGARTAL SVVTWNKDIV 250
TKITPEGAEE WSLAIPVMCL LANTTFPCSQ PPCIPCCYEK EPEETLRMLE 300
DNVMRPGYYQ LLQASLTCSP HRQRRSTKDN FNVYKATRPY LAHCPDCGEG 350
HSCHSPVALE RIRNEATDGT LKIQVSLQIG IGTDDSHDWT KLRYMDNHIP 400
ADAGRAGLFV RTSAPCTITG TMGHFILARC PKGETLTVGF TDSRKISHSC 450
THPFHHDPPV IGREKFHSRP QHGKELPCST YVQSNAATAE EIEVHMPPDT 500
PDRTLLSQQS GNVKITVNGR TVRYKCNCGG SNEGLITTDK VINNCKVDQC 550
HAAVTNHKKW QYNSPLVPRN AELGDRKGKI HIPFPLANVT CMVPKARNPT 600
VTYGKNQVIM LLYPDHPTLL SYRSMGEEPN YQEEWVTHKK EVVLTVPTEG 650
LEVTWGNNEP YKYWPQLSAN GTAHGHPHEI ILYYYELYPT MTVVVVSVAS 700
FILLSMVGMA VGMCMCARRR CITPYELTPG ATVPFLLSLI CCIRTAKAAT 750
YQEAAVYLWN EQQPLFWLQA LIPLAALIVL CNCLRLLPCC CKTLAFLAVM 800
SIGAHTVSAY EHVTVIPNTV GVPYKTLVNR PGYSPMVLEM ELLSVTLEPT 850
LSLDYITCEY KTVIPSPYVK CCGTAECKDK NLPDYSCKVF TGVYPFMWGG 900
AYCFCDAENT QLSEAHVEKS ESCKTEFASA YRAHTASASA KLRVLYQGNN 950
ITVTAYANGD HAVTVKDAKF IVGPMSSAWT PFDNKIVVYK GDVYNMDYPP 1000
FGAGRPGQFG DIQSRTPESK DVYANTQLVL QRPAAGTVHV PYSQAPSGFK 1050
YWLKERGASL QHTAPFGCQI ATNPVRAMNC AVGNMPISID IPDAAFTRVV 1100
DAPSLTDMSC EVPACTHSSD FGGVAIIKYA VSKKGKCAVH SMTNAVTIRE 1150
AEIEVEGNSQ LQISFSTALA SAEFRVQVCS TQVHCAAECH PPKDHIVNYP 1200
ASHTTLGVQD ISATAMSWVQ KITGGVGLVV AVAALILIVV LCVSFSRH 1248
Length:1,248
Mass (Da):138,114
Last modified:July 27, 2011 - v3
Checksum:i1A2CEB5671529482
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti63 – 631R → K in AAN05102. 1 Publication
Sequence conflicti519 – 5202GR → SQ in AAN05102. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF369024 Genomic RNA. Translation: AAN05102.2.
AF339485 Genomic RNA. Translation: AAO33341.1.
AF490259 Genomic RNA. Translation: AAM10747.2.
RefSeqiNP_690589.2. NC_004162.2.

Genome annotation databases

GeneIDi956308.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF369024 Genomic RNA. Translation: AAN05102.2 .
AF339485 Genomic RNA. Translation: AAO33341.1 .
AF490259 Genomic RNA. Translation: AAM10747.2 .
RefSeqi NP_690589.2. NC_004162.2.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2RSW NMR - A 893-910 [» ]
ProteinModelPortali Q8JUX5.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi S03.001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 956308.

Family and domain databases

Gene3Di 2.60.40.350. 1 hit.
2.60.98.10. 3 hits.
InterProi IPR002548. Alpha_E1_glycop.
IPR000936. Alpha_E2_glycop.
IPR002533. Alpha_E3_glycop.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014756. Ig_E-set.
IPR000930. Peptidase_S3.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view ]
Pfami PF01589. Alpha_E1_glycop. 1 hit.
PF00943. Alpha_E2_glycop. 1 hit.
PF01563. Alpha_E3_glycop. 1 hit.
PF00944. Peptidase_S3. 1 hit.
[Graphical view ]
PRINTSi PR00798. TOGAVIRIN.
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF56983. SSF56983. 1 hit.
SSF81296. SSF81296. 1 hit.
PROSITEi PS51690. ALPHAVIRUS_CP. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site."
    Khan A.H., Morita K., Parquet Md Mdel C., Hasebe F., Mathenge E.G., Igarashi A.
    J. Gen. Virol. 83:3075-3084(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Nucleotide sequence analyses of the 26S mRNAs of viruses of the genus Alphavirus."
    Kinney R.M., Pfeffer M.
    Submitted (JAN-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  3. Logue C.H., Atkins G.J.
    Submitted (OCT-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate Ross.
  4. Logue C.H., Chamberlain J.F., Atkins G.J.
    Submitted (FEB-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 91-97; 576 AND 592.

Entry informationi

Entry nameiPOLS_CHIKS
AccessioniPrimary (citable) accession number: Q8JUX5
Secondary accession number(s): Q80S29, Q8QR21
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: July 27, 2011
Last modified: May 14, 2014
This is version 82 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Structural polyprotein is translated from a subgenomic RNA synthesized during togavirus replication.

Keywords - Technical termi

3D-structure, Complete proteome, 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

External Data

Dasty 3

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