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P27285

- POLS_SINDO

UniProt

P27285 - POLS_SINDO

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
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 1 (01 Aug 1992)
      Previous versions | rss
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    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)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei141 – 1411Charge relay systemPROSITE-ProRule annotation
    Active sitei147 – 1471Charge relay systemPROSITE-ProRule annotation
    Active sitei215 – 2151Charge relay systemPROSITE-ProRule annotation
    Sitei264 – 2652Cleavage; by capsid proteinBy similarity
    Sitei328 – 3292Cleavage; by host furinBy similarity
    Sitei751 – 7522Cleavage; by host signal peptidaseBy similarity
    Sitei806 – 8072Cleavage; by host signal peptidaseBy 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

    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

    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

    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 – 751487p62By similarityPRO_0000226240Add
    BLAST
    Chaini265 – 32864E3 proteinPRO_0000041317Add
    BLAST
    Signal peptidei265 – 28016Not cleavedSequence AnalysisAdd
    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 hostSequence Analysis
    Glycosylationi524 – 5241N-linked (GlcNAc...); by hostSequence Analysis
    Glycosylationi646 – 6461N-linked (GlcNAc...); by hostSequence Analysis
    Lipidationi724 – 7241S-palmitoyl cysteine; by hostBy similarity
    Lipidationi744 – 7441S-palmitoyl cysteine; by hostBy similarity
    Lipidationi745 – 7451S-palmitoyl cysteine; by hostBy similarity
    Disulfide bondi855 ↔ 920By similarity
    Disulfide bondi868 ↔ 900By similarity
    Disulfide bondi869 ↔ 902By similarity
    Disulfide bondi874 ↔ 884By similarity
    Glycosylationi945 – 9451N-linked (GlcNAc...); by hostSequence Analysis
    Glycosylationi1051 – 10511N-linked (GlcNAc...); by hostSequence Analysis
    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.

    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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP27285.

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei696 – 71217HelicalSequence AnalysisAdd
    BLAST
    Transmembranei728 – 74619HelicalSequence AnalysisAdd
    BLAST
    Transmembranei768 – 78417HelicalSequence AnalysisAdd
    BLAST
    Transmembranei786 – 80217HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1216 – 123419HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini114 – 264151Peptidase S3PROSITE-ProRule annotationAdd
    BLAST

    Region

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

    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.
    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

    « Hide

    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: October 1, 2014
    This is version 111 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