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Protein

Structural polyprotein

Gene
N/A
Organism
Chikungunya virus (strain S27-African prototype) (CHIKV)
Status
Reviewed-Annotation score: -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 icosahedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of the spike glycoprotein E2 at the cell membrane, leading to budding and formation of mature virions. In case of infection, new virions attach to target cells and after clathrin-mediated endocytosis their membrane fuses with the host endosomal 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
Assembly protein E3: Provides the signal sequence for the translocation of the precursor of protein E3/E2 to the host endoplasmic reticulum. Mediates pH protection of spike glycoprotein E1 during the transport via the secretory pathway.By similarity
Spike glycoprotein E2: Plays a role in 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 protein: 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
Spike glycoprotein E1: 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. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.By similarity1 Publication

Miscellaneous

Structural polyprotein: Translated from a subgenomic RNA synthesized during togavirus replication.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.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei139Charge relay systemPROSITE-ProRule annotation1
Active sitei161Charge relay systemPROSITE-ProRule annotation1
Active sitei213Charge relay systemPROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Protease, Serine protease
Biological processFusion 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):
p62
pE2
Alternative name(s):
E2 envelope glycoprotein
Alternative name(s):
E1 envelope glycoprotein
OrganismiChikungunya virus (strain S27-African prototype) (CHIKV)
Taxonomic identifieri371094 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTogaviridaeAlphavirus
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]
Proteomesi
  • UP000000569 Componenti: Genome
  • UP000126290 Componenti: Genome

Subcellular locationi

Capsid protein :
  • Virion By similarity
  • Host cytoplasm By similarity
  • Host cell membrane By similarity
Spike glycoprotein E2 :
6K protein :
Spike glycoprotein E1 :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini262 – 692ExtracellularSequence analysisAdd BLAST431
Transmembranei693 – 713HelicalSequence analysisAdd BLAST21
Topological domaini714 – 748CytoplasmicSequence analysisAdd BLAST35
Topological domaini749 – 763ExtracellularSequence analysisAdd BLAST15
Transmembranei764 – 784HelicalSequence analysisAdd BLAST21
Topological domaini785 – 795CytoplasmicSequence analysisAdd BLAST11
Transmembranei796 – 816HelicalSequence analysisAdd BLAST21
Topological domaini817 – 1224ExtracellularSequence analysisAdd BLAST408
Transmembranei1225 – 1245HelicalSequence analysisAdd BLAST21
Topological domaini1246 – 1248CytoplasmicSequence analysis3

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
ChainiPRO_00002262191 – 261Capsid proteinBy similarityAdd BLAST261
ChainiPRO_0000226220262 – 748Precursor of protein E3/E2By similarityAdd BLAST487
ChainiPRO_0000226221262 – 325Assembly protein E3By similarityAdd BLAST64
ChainiPRO_0000226222326 – 748Spike glycoprotein E2By similarityAdd BLAST423
ChainiPRO_0000226223749 – 8096K proteinBy similarityAdd BLAST61
ChainiPRO_0000226224810 – 1248Spike glycoprotein E1By similarityAdd BLAST439

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi113 ↔ 128By similarity
Glycosylationi273N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi588N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi670N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Lipidationi721S-palmitoyl cysteine; by hostBy similarity1
Lipidationi741S-palmitoyl cysteine; by hostBy similarity1
Lipidationi742S-palmitoyl cysteine; by hostBy similarity1
Disulfide bondi858 ↔ 923By similarity
Disulfide bondi871 ↔ 903By similarity
Disulfide bondi872 ↔ 905By similarity
Disulfide bondi877 ↔ 887By similarity
Glycosylationi950N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Disulfide bondi1068 ↔ 1080By similarity
Disulfide bondi1110 ↔ 1185By similarity
Disulfide bondi1115 ↔ 1189By similarity
Disulfide bondi1137 ↔ 1179By similarity
Lipidationi1242S-stearoyl cysteine; by hostBy similarity1

Post-translational modificationi

Structural polyprotein: Specific enzymatic cleavages in vivo yield mature proteins. Capsid protein is auto-cleaved during polyprotein translation, unmasking a signal peptide at the N-terminus of the precursor of E3/E2. The remaining polyprotein is then targeted to the host endoplasmic reticulum, where host signal peptidase cleaves it into pE2, 6K and E1 proteins. pE2 is further processed to mature E3 and E2 by host furin in trans-Golgi vesicle.By similarity
Spike glycoprotein E2: 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.By similarity
Spike glycoprotein E1: N-glycosylated.By similarity
Spike glycoprotein E2: N-glycosylated.By similarity
Assembly protein E3: N-glycosylated.By similarity
6K protein: Palmitoylated via thioester bonds.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei261 – 262Cleavage; by autolysisBy similarity2
Sitei325 – 326Cleavage; by host furinBy similarity2
Sitei748 – 749Cleavage; by host signal peptidaseBy similarity2
Sitei809 – 810Cleavage; by host signal peptidaseBy similarity2

Keywords - PTMi

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

Interactioni

Subunit structurei

Precursor of protein E3/E2: The precursor of protein E3/E2 and E1 form a heterodimer shortly after synthesis. Spike glycoprotein E1: The precursor of protein E3/E2 and E1 form a heterodimer shortly after synthesis. Spike glycoprotein E1: Processing of the precursor of protein E3/E2 into E2 and E3 results in a heterodimer of the spike glycoproteins E2 and E1. Spike glycoprotein E2: Processing of the precursor of protein E3/E2 into E2 and E3 results in a heterodimer of the spike glycoproteins E2 and E1. Spike glycoprotein E1: Spike at virion surface are constituted of three E2-E1 heterodimers. Spike glycoprotein E2: Spike at virion surface are constituted of three E2-E1 heterodimers. Spike glycoprotein E1: After target cell attachment and endocytosis, E1 change conformation to form homotrimers. 6K protein: Interacts with spike glycoprotein E1. 6K protein: Interacts with spike glycoprotein E2. Spike glycoprotein E1: Interacts with 6K protein. Spike glycoprotein E2: Interacts with 6K protein.By similarity

Structurei

Secondary structure

11248
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi895 – 899Combined sources5
Turni904 – 907Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2RSWNMR-A893-910[»]
ProteinModelPortaliQ8JUX5
SMRiQ8JUX5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini113 – 261Peptidase S3PROSITE-ProRule annotationAdd BLAST149

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 107Intrinsically disordered, in contact with genomic RNA in nucleocapsidSequence analysisAdd BLAST107
Regioni91 – 100Ribosome-bindingBy similarity10
Regioni262 – 274Functions as an uncleaved signal peptide for the precursor of protein E3/E2By similarityAdd BLAST13
Regioni721 – 741Transient transmembrane before p62-6K protein processingSequence analysisAdd BLAST21
Regioni893 – 910E1 fusion peptide loop1 PublicationAdd BLAST18

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi60 – 98Lys-richAdd BLAST39
Compositional biasi95 – 98Poly-LysSequence analysis4
Compositional biasi693 – 698Poly-ValSequence analysis6

Domaini

Structural polyprotein: As soon as the capsid protein has been autocleaved, an internal uncleaved signal peptide directs the remaining polyprotein to the endoplasmic reticulum.By similarity

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

KOiK19288
OrthoDBiVOG0900007W

Family and domain databases

Gene3Di2.60.40.350, 1 hit
2.60.98.10, 3 hits
InterProiView protein in InterPro
IPR002548 Alpha_E1_glycop
IPR000936 Alpha_E2_glycop
IPR002533 Alpha_E3_glycop
IPR000336 Flavivir/Alphavir_Ig-like_sf
IPR036253 Glycoprot_cen/dimer_sf
IPR038055 Glycoprot_E_dimer_dom
IPR014756 Ig_E-set
IPR009003 Peptidase_S1_PA
IPR000930 Peptidase_S3
PfamiView protein in Pfam
PF01589 Alpha_E1_glycop, 1 hit
PF00943 Alpha_E2_glycop, 1 hit
PF01563 Alpha_E3_glycop, 1 hit
PF00944 Peptidase_S3, 1 hit
PRINTSiPR00798 TOGAVIRIN
SUPFAMiSSF50494 SSF50494, 1 hit
SSF56983 SSF56983, 1 hit
SSF81296 SSF81296, 1 hit
PROSITEiView protein in PROSITE
PS51690 ALPHAVIRUS_CP, 1 hit

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

Isoform Structural polyprotein (identifier: Q8JUX5-1) [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
MEFIPTQTFY NRRYQPRPWT PRPTIQVIRP RPRPQRQAGQ LAQLISAVNK
60 70 80 90 100
LTMRAVPQQK PRRNRKNKKQ KQKQQAPQNN TNQKKQPPKK KPAQKKKKPG
110 120 130 140 150
RRERMCMKIE NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA
160 170 180 190 200
KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGGR
210 220 230 240 250
FTIPTGAGKP GDSGRPIFDN KGRVVAIVLG GANEGARTAL SVVTWNKDIV
260 270 280 290 300
TKITPEGAEE WSLAIPVMCL LANTTFPCSQ PPCIPCCYEK EPEETLRMLE
310 320 330 340 350
DNVMRPGYYQ LLQASLTCSP HRQRRSTKDN FNVYKATRPY LAHCPDCGEG
360 370 380 390 400
HSCHSPVALE RIRNEATDGT LKIQVSLQIG IGTDDSHDWT KLRYMDNHIP
410 420 430 440 450
ADAGRAGLFV RTSAPCTITG TMGHFILARC PKGETLTVGF TDSRKISHSC
460 470 480 490 500
THPFHHDPPV IGREKFHSRP QHGKELPCST YVQSNAATAE EIEVHMPPDT
510 520 530 540 550
PDRTLLSQQS GNVKITVNGR TVRYKCNCGG SNEGLITTDK VINNCKVDQC
560 570 580 590 600
HAAVTNHKKW QYNSPLVPRN AELGDRKGKI HIPFPLANVT CMVPKARNPT
610 620 630 640 650
VTYGKNQVIM LLYPDHPTLL SYRSMGEEPN YQEEWVTHKK EVVLTVPTEG
660 670 680 690 700
LEVTWGNNEP YKYWPQLSAN GTAHGHPHEI ILYYYELYPT MTVVVVSVAS
710 720 730 740 750
FILLSMVGMA VGMCMCARRR CITPYELTPG ATVPFLLSLI CCIRTAKAAT
760 770 780 790 800
YQEAAVYLWN EQQPLFWLQA LIPLAALIVL CNCLRLLPCC CKTLAFLAVM
810 820 830 840 850
SIGAHTVSAY EHVTVIPNTV GVPYKTLVNR PGYSPMVLEM ELLSVTLEPT
860 870 880 890 900
LSLDYITCEY KTVIPSPYVK CCGTAECKDK NLPDYSCKVF TGVYPFMWGG
910 920 930 940 950
AYCFCDAENT QLSEAHVEKS ESCKTEFASA YRAHTASASA KLRVLYQGNN
960 970 980 990 1000
ITVTAYANGD HAVTVKDAKF IVGPMSSAWT PFDNKIVVYK GDVYNMDYPP
1010 1020 1030 1040 1050
FGAGRPGQFG DIQSRTPESK DVYANTQLVL QRPAAGTVHV PYSQAPSGFK
1060 1070 1080 1090 1100
YWLKERGASL QHTAPFGCQI ATNPVRAMNC AVGNMPISID IPDAAFTRVV
1110 1120 1130 1140 1150
DAPSLTDMSC EVPACTHSSD FGGVAIIKYA VSKKGKCAVH SMTNAVTIRE
1160 1170 1180 1190 1200
AEIEVEGNSQ LQISFSTALA SAEFRVQVCS TQVHCAAECH PPKDHIVNYP
1210 1220 1230 1240
ASHTTLGVQD ISATAMSWVQ KITGGVGLVV AVAALILIVV LCVSFSRH
Note: Produced by conventional translation.
Length:1,248
Mass (Da):138,114
Last modified:July 27, 2011 - v3
Checksum:i1A2CEB5671529482
GO
Isoform Frameshifted structural polyprotein (identifier: P0DOK1-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0DOK1.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by ribosomal frameshifting.
Length:824
Mass (Da):92,620
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti63R → K in AAN05102 (PubMed:12466484).Curated1
Sequence conflicti519 – 520GR → SQ in AAN05102 (PubMed:12466484).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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
KEGGivg:956308

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Similar proteinsi

Entry informationi

Entry nameiPOLS_CHIKS
AccessioniPrimary (citable) accession number: Q8JUX5
Secondary accession number(s): Q80S29, Q8QR21
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: July 27, 2011
Last modified: April 25, 2018
This is version 100 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health