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P27285

- POLS_SINDO

UniProt

P27285 - POLS_SINDO

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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: 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 sitei141 – 1411Charge relay system By similarity
Active sitei147 – 1471Charge relay system By similarity
Active sitei215 – 2151Charge relay system By similarity
Sitei264 – 2652Cleavage; by capsid protein By similarity
Sitei328 – 3292Cleavage; by host furin By similarity
Sitei751 – 7522Cleavage; by host signal peptidase By similarity
Sitei806 – 8072Cleavage; 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

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 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]
ProteomesiUP000006561: Genome

Subcellular locationi

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei696 – 71217Helical; Reviewed predictionAdd
BLAST
Transmembranei728 – 74619Helical; Reviewed predictionAdd
BLAST
Transmembranei768 – 78417Helical; Reviewed predictionAdd
BLAST
Transmembranei786 – 80217Helical; Reviewed predictionAdd
BLAST
Transmembranei1216 – 123419Helical; Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-SubCell
  2. host cell plasma membrane Source: UniProtKB-SubCell
  3. integral component of membrane Source: UniProtKB-KW
  4. T=4 icosahedral viral capsid 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 – 264264Capsid proteinPRO_0000041316Add
BLAST
Chaini265 – 751487p62 By similarityPRO_0000226240Add
BLAST
Chaini265 – 32864E3 proteinPRO_0000041317Add
BLAST
Signal peptidei265 – 28016Not cleaved Reviewed predictionAdd
BLAST
Chaini329 – 751423E2 envelope glycoproteinPRO_0000041318Add
BLAST
Chaini752 – 806556K proteinPRO_0000041319Add
BLAST
Chaini807 – 1245439E1 envelope glycoproteinPRO_0000041320Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi278 – 2781N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi524 – 5241N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi646 – 6461N-linked (GlcNAc...); by host Reviewed prediction
Lipidationi724 – 7241S-palmitoyl cysteine; by host By similarity
Lipidationi744 – 7441S-palmitoyl cysteine; by host By similarity
Lipidationi745 – 7451S-palmitoyl cysteine; by host By similarity
Disulfide bondi855 ↔ 920 By similarity
Disulfide bondi868 ↔ 900 By similarity
Disulfide bondi869 ↔ 902 By similarity
Disulfide bondi874 ↔ 884 By similarity
Glycosylationi945 – 9451N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi1051 – 10511N-linked (GlcNAc...); by host Reviewed prediction
Disulfide bondi1065 ↔ 1077 By similarity
Disulfide bondi1107 ↔ 1182 By similarity
Disulfide bondi1112 ↔ 1186 By similarity
Disulfide bondi1134 ↔ 1176 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 and 6K are palmitoylated via thioester bonds.

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

1
1245
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi115 – 1195
Beta strandi125 – 1328
Beta strandi135 – 1395
Beta strandi144 – 1485
Helixi151 – 1533
Beta strandi157 – 1593
Helixi160 – 1623
Beta strandi164 – 1685
Turni171 – 1766
Beta strandi186 – 1916
Beta strandi194 – 1996
Beta strandi202 – 2065
Beta strandi218 – 2203
Beta strandi226 – 23611
Beta strandi239 – 2479
Beta strandi253 – 2564

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WYKX-ray2.00A/B/C/D114-264[»]
DisProtiDP00066.
ProteinModelPortaliP27285.
SMRiP27285. Positions 106-264, 691-726, 807-1096, 1101-1189, 1215-1245.

Miscellaneous databases

EvolutionaryTraceiP27285.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini114 – 264151Peptidase S3Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni93 – 1019Ribosome-binding By similarity

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.

P27285-1 [UniParc]FASTAAdd to Basket

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MNRGFFNMLG RRPFPAPTAM WRPRRRRQAA PMPARNGLAS QIQQLTTAVS     50
ALVIGQATRP QNPRPRPPPR QKKQAPKQPP KPKKPKPQEK KKKQPAKTKP 100
GKRQRMALKL EADRLFDVKN EDGDVIGHAL AMEGKVMKPL HVKGTIDHPV 150
LSKLKFTKSS AYDMEFAQLP VNMRSEAFTY TSEHPEGFYN WHHGAVQYSG 200
GRFTIPRGVG GRGDSGRPIM DNSGRVVAIV LGGADEGTRT ALSVVTWNSK 250
GKTIKTTPEG TEEWSAAPLV TAMCLLGNVS FPCNRPPTCY TREPSRALDI 300
LEENVNHEAY DTLLNAILRC GSSGRSKRSV TDDFTLTSPY LGTCSYCHHT 350
EPCFSPIKIE QVWDEADDNT IRIQTSAQFG YDKSGAASTN KYRYMSFEQD 400
HTVKEGTMDD IKISTSGPCR RLSYKGYFLL AKCPPGDSVT VSIASSNSAT 450
SCTMARKIKP KFVGREKYDL PPVHGKKIPC TVYDRLKETT AGYITMHRPG 500
PHAYTSYLEE SSGKVYAKPP SGKNITYECK CGDYKTGTVT TRTEITGCTA 550
IKQCVAYKSD QTKWVFNSPD LIRHADHTAQ GKLHLPFKLI PSTCMVPVAH 600
APNVIHGFKH ISLQLDTDHL TLLTTRRLGA NPEPTTEWII GKTVRNFTVD 650
RDGLEYIWGN HEPVRVYAQE SAPGDPHGWP HEIVQHYYHR HPVYTILAVA 700
SAAVAMMIGV TVAALCACKA RRECLTPYAL APNAVIPTSL ALLCCVRSAN 750
AETFTETMSY FWSNSQPFFW VQLCIPLAAV IVLMRCCSCC LPFLVVAGAY 800
LAKVDAYEHA TTVPNVPQIP YKALVERAGY APLNLEITVM SSEVLPSTNQ 850
EYITCKFTTV VPSPKVKCCG SLECQPAAHA DYTCKVFGGV YPFMWGGAQC 900
FCDSENSQMS EAYVELSADC ATDHAQAIKV HTAAMKVGLR IVYGNTTSFL 950
DVYVNGVTPG TSKDLKVIAG PISASFTPFD HKVVIHRGLV YNYDFPEYGA 1000
MKPGVFGDIQ ATSLTSKDLI ASTDIRLLKP SAKNVHVPYT QAASGFEMWK 1050
NNSGRPLQET APFGCKIAVN PLRAVDCSYG NIPISIDIPN AAFIRTSDAP 1100
LVSTVKCDVS ECTYSADFGG MATLQYVSDR EGQCPVHSHS STATLQESTV 1150
HVLEKGAVTV HFSTASPQAN FIVSLCGKKT TCNAECKPPA DHIVSTPHKN 1200
DQEFQAAISK TSWSWLFALF GGASSLLIIG LTIFACSMML TSTRR 1245
Length:1,245
Mass (Da):136,650
Last modified:August 1, 1992 - v1
Checksum:i967EF00E675F84EF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M69205 Genomic RNA. Translation: AAA96973.1.
M69207 Genomic RNA. Translation: AAA73066.1.
PIRiB39991. VHWV82.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M69205 Genomic RNA. Translation: AAA96973.1 .
M69207 Genomic RNA. Translation: AAA73066.1 .
PIRi B39991. VHWV82.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1WYK X-ray 2.00 A/B/C/D 114-264 [» ]
DisProti DP00066.
ProteinModelPortali P27285.
SMRi P27285. Positions 106-264, 691-726, 807-1096, 1101-1189, 1215-1245.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P27285.

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. "Structure of the Ockelbo virus genome and its relationship to other Sindbis viruses."
    Shirako Y., Niklasson B., Dalrymple J.M., Strauss E.G., Strauss J.H.
    Virology 182:753-764(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

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: May 14, 2014
This is version 110 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

External Data

Dasty 3

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