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P27285 (POLS_SINDO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Structural polyprotein
Alternative name(s):
p130

Cleaved into the following 6 chains:

  1. Capsid protein
    EC=3.4.21.90
    Alternative name(s):
    Coat protein
    Short name=C
  2. p62
    Alternative name(s):
    E3/E2
  3. E3 protein
    Alternative name(s):
    Spike glycoprotein E3
  4. E2 envelope glycoprotein
    Alternative name(s):
    Spike glycoprotein E2
  5. 6K protein
  6. E1 envelope glycoprotein
    Alternative name(s):
    Spike glycoprotein E1
OrganismSindbis virus subtype Ockelbo (strain Edsbyn 82-5) (OCKV) (Ockelbo virus) [Complete proteome]
Taxonomic identifier31699 [NCBI]
Taxonomic lineageViruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus › WEEV complex ›
Virus hostAcrocephalus scirpaceus [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]

Protein attributes

Sequence length1245 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Subunit structure

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.

Subcellular location

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

p62: Virion membrane; Single-pass type I membrane protein By similarity. Host cell membrane; Single-pass type I membrane protein By similarity.

E2 envelope glycoprotein: Virion membrane; Single-pass type I membrane protein By similarity. Host cell membrane; Single-pass type I membrane protein By similarity.

E1 envelope glycoprotein: Virion membrane; Single-pass type I membrane protein By similarity. Host cell membrane; Single-pass type I membrane protein By similarity.

6K protein: Host cell membrane; Multi-pass membrane protein By similarity. Virion membrane; Multi-pass membrane protein By similarity.

Post-translational modification

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.

Miscellaneous

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

Sequence similarities

Contains 1 peptidase S3 domain.

Ontologies

Keywords
   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
   Cellular componentHost cell membrane
Host cytoplasm
Host membrane
Membrane
Virion
   DomainSignal
Transmembrane
Transmembrane helix
   Molecular functionCapsid protein
Hydrolase
Protease
Serine protease
T=4 icosahedral capsid protein
   PTMCleavage on pair of basic residues
Disulfide bond
Glycoprotein
Lipoprotein
Palmitate
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processproteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

viral attachment to host cell

Inferred from electronic annotation. Source: UniProtKB-KW

viral entry into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentT=4 icosahedral viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

host cell cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral to membrane

Inferred from electronic annotation. Source: UniProtKB-KW

virion membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionserine-type endopeptidase activity

Inferred from electronic annotation. Source: InterPro

structural molecule activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 264264Capsid protein
PRO_0000041316
Chain265 – 751487p62 By similarity
PRO_0000226240
Chain265 – 32864E3 protein
PRO_0000041317
Signal peptide265 – 28016Not cleaved Potential
Chain329 – 751423E2 envelope glycoprotein
PRO_0000041318
Chain752 – 806556K protein
PRO_0000041319
Chain807 – 1245439E1 envelope glycoprotein
PRO_0000041320

Regions

Transmembrane696 – 71217Helical; Potential
Transmembrane728 – 74619Helical; Potential
Transmembrane768 – 78417Helical; Potential
Transmembrane786 – 80217Helical; Potential
Transmembrane1216 – 123419Helical; Potential
Domain107 – 264158Peptidase S3
Region93 – 1019Ribosome-binding By similarity

Sites

Active site1411Charge relay system By similarity
Active site1471Charge relay system By similarity
Active site2151Charge relay system By similarity
Site264 – 2652Cleavage; by capsid protein By similarity
Site328 – 3292Cleavage; by host furin By similarity
Site751 – 7522Cleavage; by host signal peptidase By similarity
Site806 – 8072Cleavage; by host signal peptidase By similarity

Amino acid modifications

Lipidation7241S-palmitoyl cysteine; by host
Lipidation7441S-palmitoyl cysteine; by host
Lipidation7451S-palmitoyl cysteine; by host
Glycosylation2781N-linked (GlcNAc...); by host Potential
Glycosylation5241N-linked (GlcNAc...); by host Potential
Glycosylation6461N-linked (GlcNAc...); by host Potential
Glycosylation9451N-linked (GlcNAc...); by host Potential
Glycosylation10511N-linked (GlcNAc...); by host Potential
Disulfide bond855 ↔ 920 By similarity
Disulfide bond868 ↔ 900 By similarity
Disulfide bond869 ↔ 902 By similarity
Disulfide bond874 ↔ 884 By similarity
Disulfide bond1065 ↔ 1077 By similarity
Disulfide bond1107 ↔ 1182 By similarity
Disulfide bond1112 ↔ 1186 By similarity
Disulfide bond1134 ↔ 1176 By similarity

Secondary structure

1 ................................ 1245
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P27285 [UniParc].

Last modified August 1, 1992. Version 1.
Checksum: 967EF00E675F84EF

FASTA1,245136,650
        10         20         30         40         50         60 
MNRGFFNMLG RRPFPAPTAM WRPRRRRQAA PMPARNGLAS QIQQLTTAVS ALVIGQATRP 

        70         80         90        100        110        120 
QNPRPRPPPR QKKQAPKQPP KPKKPKPQEK KKKQPAKTKP GKRQRMALKL EADRLFDVKN 

       130        140        150        160        170        180 
EDGDVIGHAL AMEGKVMKPL HVKGTIDHPV LSKLKFTKSS AYDMEFAQLP VNMRSEAFTY 

       190        200        210        220        230        240 
TSEHPEGFYN WHHGAVQYSG GRFTIPRGVG GRGDSGRPIM DNSGRVVAIV LGGADEGTRT 

       250        260        270        280        290        300 
ALSVVTWNSK GKTIKTTPEG TEEWSAAPLV TAMCLLGNVS FPCNRPPTCY TREPSRALDI 

       310        320        330        340        350        360 
LEENVNHEAY DTLLNAILRC GSSGRSKRSV TDDFTLTSPY LGTCSYCHHT EPCFSPIKIE 

       370        380        390        400        410        420 
QVWDEADDNT IRIQTSAQFG YDKSGAASTN KYRYMSFEQD HTVKEGTMDD IKISTSGPCR 

       430        440        450        460        470        480 
RLSYKGYFLL AKCPPGDSVT VSIASSNSAT SCTMARKIKP KFVGREKYDL PPVHGKKIPC 

       490        500        510        520        530        540 
TVYDRLKETT AGYITMHRPG PHAYTSYLEE SSGKVYAKPP SGKNITYECK CGDYKTGTVT 

       550        560        570        580        590        600 
TRTEITGCTA IKQCVAYKSD QTKWVFNSPD LIRHADHTAQ GKLHLPFKLI PSTCMVPVAH 

       610        620        630        640        650        660 
APNVIHGFKH ISLQLDTDHL TLLTTRRLGA NPEPTTEWII GKTVRNFTVD RDGLEYIWGN 

       670        680        690        700        710        720 
HEPVRVYAQE SAPGDPHGWP HEIVQHYYHR HPVYTILAVA SAAVAMMIGV TVAALCACKA 

       730        740        750        760        770        780 
RRECLTPYAL APNAVIPTSL ALLCCVRSAN AETFTETMSY FWSNSQPFFW VQLCIPLAAV 

       790        800        810        820        830        840 
IVLMRCCSCC LPFLVVAGAY LAKVDAYEHA TTVPNVPQIP YKALVERAGY APLNLEITVM 

       850        860        870        880        890        900 
SSEVLPSTNQ EYITCKFTTV VPSPKVKCCG SLECQPAAHA DYTCKVFGGV YPFMWGGAQC 

       910        920        930        940        950        960 
FCDSENSQMS EAYVELSADC ATDHAQAIKV HTAAMKVGLR IVYGNTTSFL DVYVNGVTPG 

       970        980        990       1000       1010       1020 
TSKDLKVIAG PISASFTPFD HKVVIHRGLV YNYDFPEYGA MKPGVFGDIQ ATSLTSKDLI 

      1030       1040       1050       1060       1070       1080 
ASTDIRLLKP SAKNVHVPYT QAASGFEMWK NNSGRPLQET APFGCKIAVN PLRAVDCSYG 

      1090       1100       1110       1120       1130       1140 
NIPISIDIPN AAFIRTSDAP LVSTVKCDVS ECTYSADFGG MATLQYVSDR EGQCPVHSHS 

      1150       1160       1170       1180       1190       1200 
STATLQESTV HVLEKGAVTV HFSTASPQAN FIVSLCGKKT TCNAECKPPA DHIVSTPHKN 

      1210       1220       1230       1240 
DQEFQAAISK TSWSWLFALF GGASSLLIIG LTIFACSMML TSTRR

« Hide

References

[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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M69205 Genomic RNA. Translation: AAA96973.1.
M69207 Genomic RNA. Translation: AAA73066.1.
PIRVHWV82. B39991.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WYKX-ray2.00A/B/C/D114-264[»]
DisProtDP00066.
ProteinModelPortalP27285.
SMRP27285. Positions 106-264, 691-726, 807-1096, 1101-1189, 1215-1245.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D2.60.40.350. 1 hit.
2.60.98.10. 3 hits.
InterProIPR002548. 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]
PfamPF01589. Alpha_E1_glycop. 1 hit.
PF00943. Alpha_E2_glycop. 1 hit.
PF01563. Alpha_E3_glycop. 1 hit.
PF00944. Peptidase_S3. 1 hit.
[Graphical view]
PRINTSPR00798. TOGAVIRIN.
SUPFAMSSF56983. Flavi_glycoprotE. 1 hit.
SSF81296. Ig_E-set. 1 hit.
SSF50494. Pept_Ser_Cys. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP27285.

Entry information

Entry namePOLS_SINDO
AccessionPrimary (citable) accession number: P27285
Secondary accession number(s): Q00349
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: May 1, 2013
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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