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Protein

Structural polyprotein

Gene
N/A
Organism
Sindbis virus subtype Ockelbo (strain Edsbyn 82-5) (OCKV) (Ockelbo virus)
Status
Reviewed-Annotation score: 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).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).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).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).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)DescriptionActionsGraphical viewLength
Active sitei141Charge relay systemPROSITE-ProRule annotation1
Active sitei147Charge relay systemPROSITE-ProRule annotation1
Active sitei215Charge relay systemPROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

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

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
OrganismiSindbis virus subtype Ockelbo (strain Edsbyn 82-5) (OCKV) (Ockelbo virus)
Taxonomic identifieri31699 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTogaviridaeAlphavirusWEEV complex
Virus hostiAcrocephalus scirpaceus (Eurasian reed-warbler) [TaxID: 48156]
Aedes [TaxID: 7158]
Culex [TaxID: 53527]
Homo sapiens (Human) [TaxID: 9606]
Motacilla alba (White wagtail) (Pied wagtail) [TaxID: 45807]
Streptopelia turtur [TaxID: 177155]
Proteomesi
  • UP000006561 Componenti: Genome

Subcellular locationi

Capsid protein :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei696 – 712HelicalSequence analysisAdd BLAST17
Transmembranei728 – 746HelicalSequence analysisAdd BLAST19
Transmembranei768 – 784HelicalSequence analysisAdd BLAST17
Transmembranei786 – 802HelicalSequence analysisAdd BLAST17
Transmembranei1216 – 1234HelicalSequence analysisAdd BLAST19

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000413161 – 264Capsid proteinAdd BLAST264
ChainiPRO_0000226240265 – 751p62By similarityAdd BLAST487
ChainiPRO_0000041317265 – 328E3 proteinAdd BLAST64
Signal peptidei265 – 280Not cleavedSequence analysisAdd BLAST16
ChainiPRO_0000041318329 – 751E2 envelope glycoproteinAdd BLAST423
ChainiPRO_0000041319752 – 8066K proteinAdd BLAST55
ChainiPRO_0000041320807 – 1245E1 envelope glycoproteinAdd BLAST439

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi278N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi524N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi646N-linked (GlcNAc...); by hostSequence analysis1
Lipidationi724S-palmitoyl cysteine; by hostBy similarity1
Lipidationi744S-palmitoyl cysteine; by hostBy similarity1
Lipidationi745S-palmitoyl cysteine; by hostBy similarity1
Disulfide bondi855 ↔ 920By similarity
Disulfide bondi868 ↔ 900By similarity
Disulfide bondi869 ↔ 902By similarity
Disulfide bondi874 ↔ 884By similarity
Glycosylationi945N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi1051N-linked (GlcNAc...); by hostSequence analysis1
Disulfide bondi1065 ↔ 1077By similarity
Disulfide bondi1107 ↔ 1182By similarity
Disulfide bondi1112 ↔ 1186By similarity
Disulfide bondi1134 ↔ 1176By 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).By similarity
E2 and 6K are palmitoylated via thioester bonds.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei264 – 265Cleavage; by capsid proteinBy similarity2
Sitei328 – 329Cleavage; by host furinBy similarity2
Sitei751 – 752Cleavage; by host signal peptidaseBy similarity2
Sitei806 – 807Cleavage; by host signal peptidaseBy similarity2

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).By similarity

Structurei

Secondary structure

11245
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi115 – 119Combined sources5
Beta strandi125 – 132Combined sources8
Beta strandi135 – 139Combined sources5
Beta strandi144 – 148Combined sources5
Helixi151 – 153Combined sources3
Beta strandi157 – 159Combined sources3
Helixi160 – 162Combined sources3
Beta strandi164 – 168Combined sources5
Turni171 – 176Combined sources6
Beta strandi186 – 191Combined sources6
Beta strandi194 – 199Combined sources6
Beta strandi202 – 206Combined sources5
Beta strandi218 – 220Combined sources3
Beta strandi226 – 236Combined sources11
Beta strandi239 – 247Combined sources9
Beta strandi253 – 256Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WYKX-ray2.00A/B/C/D114-264[»]
DisProtiDP00066.
ProteinModelPortaliP27285.
SMRiP27285.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP27285.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini114 – 264Peptidase S3PROSITE-ProRule annotationAdd BLAST151

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni93 – 101Ribosome-bindingBy similarity9

Sequence similaritiesi

Contains 1 peptidase S3 domain.PROSITE-ProRule annotation

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.
IPR009003. Peptidase_S1_PA.
IPR000930. Peptidase_S3.
[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.

P27285-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNRGFFNMLG RRPFPAPTAM WRPRRRRQAA PMPARNGLAS QIQQLTTAVS
60 70 80 90 100
ALVIGQATRP QNPRPRPPPR QKKQAPKQPP KPKKPKPQEK KKKQPAKTKP
110 120 130 140 150
GKRQRMALKL EADRLFDVKN EDGDVIGHAL AMEGKVMKPL HVKGTIDHPV
160 170 180 190 200
LSKLKFTKSS AYDMEFAQLP VNMRSEAFTY TSEHPEGFYN WHHGAVQYSG
210 220 230 240 250
GRFTIPRGVG GRGDSGRPIM DNSGRVVAIV LGGADEGTRT ALSVVTWNSK
260 270 280 290 300
GKTIKTTPEG TEEWSAAPLV TAMCLLGNVS FPCNRPPTCY TREPSRALDI
310 320 330 340 350
LEENVNHEAY DTLLNAILRC GSSGRSKRSV TDDFTLTSPY LGTCSYCHHT
360 370 380 390 400
EPCFSPIKIE QVWDEADDNT IRIQTSAQFG YDKSGAASTN KYRYMSFEQD
410 420 430 440 450
HTVKEGTMDD IKISTSGPCR RLSYKGYFLL AKCPPGDSVT VSIASSNSAT
460 470 480 490 500
SCTMARKIKP KFVGREKYDL PPVHGKKIPC TVYDRLKETT AGYITMHRPG
510 520 530 540 550
PHAYTSYLEE SSGKVYAKPP SGKNITYECK CGDYKTGTVT TRTEITGCTA
560 570 580 590 600
IKQCVAYKSD QTKWVFNSPD LIRHADHTAQ GKLHLPFKLI PSTCMVPVAH
610 620 630 640 650
APNVIHGFKH ISLQLDTDHL TLLTTRRLGA NPEPTTEWII GKTVRNFTVD
660 670 680 690 700
RDGLEYIWGN HEPVRVYAQE SAPGDPHGWP HEIVQHYYHR HPVYTILAVA
710 720 730 740 750
SAAVAMMIGV TVAALCACKA RRECLTPYAL APNAVIPTSL ALLCCVRSAN
760 770 780 790 800
AETFTETMSY FWSNSQPFFW VQLCIPLAAV IVLMRCCSCC LPFLVVAGAY
810 820 830 840 850
LAKVDAYEHA TTVPNVPQIP YKALVERAGY APLNLEITVM SSEVLPSTNQ
860 870 880 890 900
EYITCKFTTV VPSPKVKCCG SLECQPAAHA DYTCKVFGGV YPFMWGGAQC
910 920 930 940 950
FCDSENSQMS EAYVELSADC ATDHAQAIKV HTAAMKVGLR IVYGNTTSFL
960 970 980 990 1000
DVYVNGVTPG TSKDLKVIAG PISASFTPFD HKVVIHRGLV YNYDFPEYGA
1010 1020 1030 1040 1050
MKPGVFGDIQ ATSLTSKDLI ASTDIRLLKP SAKNVHVPYT QAASGFEMWK
1060 1070 1080 1090 1100
NNSGRPLQET APFGCKIAVN PLRAVDCSYG NIPISIDIPN AAFIRTSDAP
1110 1120 1130 1140 1150
LVSTVKCDVS ECTYSADFGG MATLQYVSDR EGQCPVHSHS STATLQESTV
1160 1170 1180 1190 1200
HVLEKGAVTV HFSTASPQAN FIVSLCGKKT TCNAECKPPA DHIVSTPHKN
1210 1220 1230 1240
DQEFQAAISK TSWSWLFALF GGASSLLIIG LTIFACSMML TSTRR
Length:1,245
Mass (Da):136,650
Last modified:August 1, 1992 - v1
Checksum:i967EF00E675F84EF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M69205 Genomic RNA. Translation: AAA96973.1.
M69207 Genomic RNA. Translation: AAA73066.1.
PIRiB39991. VHWV82.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M69205 Genomic RNA. Translation: AAA96973.1.
M69207 Genomic RNA. Translation: AAA73066.1.
PIRiB39991. VHWV82.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WYKX-ray2.00A/B/C/D114-264[»]
DisProtiDP00066.
ProteinModelPortaliP27285.
SMRiP27285.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP27285.

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.
IPR009003. Peptidase_S1_PA.
IPR000930. Peptidase_S3.
[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]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLS_SINDO
AccessioniPrimary (citable) accession number: P27285
Secondary accession number(s): Q00349
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: November 2, 2016
This is version 119 of the entry and version 1 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

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.