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P08563 (POLS_RUBVM) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 83. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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):
p110

Cleaved into the following 3 chains:

  1. Capsid protein
    Alternative name(s):
    Coat protein
    Short name=C
  2. E2 envelope glycoprotein
    Alternative name(s):
    Spike glycoprotein E2
  3. E1 envelope glycoprotein
    Alternative name(s):
    Spike glycoprotein E1
OrganismRubella virus (strain M33) (RUBV) [Complete proteome]
Taxonomic identifier11043 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageTogaviridaeRubivirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length1063 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 interacts with genomic RNA and 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. Phosphorylation negatively regulates RNA-binding activity, possibly delaying virion assembly during the viral replication phase. Capsid protein dimerizes and becomes disulfide-linked in the virion, but this interaction seems not to be important for its biological function. Modulates genomic RNA replication. Modulates subgenomic RNA synthesis by interacting with human C1QBP/SF2P32. Induces both perinuclear clustering of mitochondria and the formation of electron-dense intermitochondrial plaques, both hallmarks of rubella virus infected cells. Induces apoptosis when expressed in transfected cells. Ref.14 Ref.15

E2 envelope glycoprotein is responsible for viral attachment to target host cell, by binding to the cell receptor. Its transport to the plasma membrane depends on interaction with E1 protein. Ref.14 Ref.15

E1 envelope glycoprotein 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 clathrin-mediated endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 homotrimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion By similarity. E1 cytoplasmic tail modulates virus release, and the tyrosines residues are critical for this function. Ref.14 Ref.15

Subunit structure

Capsid protein homooligomerizes. Forms a dimer shortly after synthesis, this dimer become disulfide-linked in the virion. Interacts with human C1QBP. E1 and E2 envelope glycoproteins heterodimerize. Ref.11

Subcellular location

Capsid protein: Virion. Host cytoplasm. Host mitochondrion. Note: The capsid protein is concentrated around Golgi region. Ref.5 Ref.6 Ref.8

E1 envelope glycoprotein: Virion membrane; Single-pass type I membrane protein. Host Golgi apparatus membrane; Single-pass type I membrane protein. Note: E1 and E2 form heterodimer in the endoplasmic reticulum before they are transported to and retained in the Golgi complex, where virus assembly occurs. E1 possesses an endoplasmic reticulum retention signal, and unassembled E2 and E1 subunits are retained in the endoplasmic reticulum. Presumably, assembly of E2 and E1 would mask the signal, thereby allowing transport of the heterodimer to the Golgi complex. Ref.5 Ref.6 Ref.8

E2 envelope glycoprotein: Virion membrane; Single-pass type I membrane protein. Host Golgi apparatus membrane; Single-pass type I membrane protein. Note: E1 and E2 form heterodimer in the endoplasmic reticulum before they are transported to and retained in the Golgi complex, where virus assembly occurs. E1 possesses an endoplasmic reticulum retention signal, and unassembled E2 and E1 subunits are retained in the endoplasmic reticulum. Presumably, assembly of E2 and E1 would mask the signal, thereby allowing transport of the heterodimer to the Golgi complex. Ref.5 Ref.6 Ref.8

Domain

The signal peptide at the C-terminus remains bound to the mature capsid protein. It may have a role as an anchor peptide, localizing the capsid assembly at the Golgi complex, where budding occurs.

Post-translational modification

Specific enzymatic cleavages in vivo yield mature proteins. An internal signal peptide at the capsid C-terminus directs E2-E1 sequences of the polyprotein precursor to the endoplasmic reticulum. Signal peptidase cleaves the precursor between Capsid and E2, releasing the capsid in the cytoplasm and the E2 N-terminus in ER. Another signal peptide at E2 C-terminus directs E1 to the ER, with a similar mechanism.

Capsid is phosphorylated on Ser-46 by host. This phosphorylation negatively regulates capsid protein RNA-binding activity. Dephosphorylated by human PP1A By similarity. Ref.17

Miscellaneous

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

Sequence caution

The sequence CAA28880.1 differs from that shown. Reason: Frameshift at several positions.

Ontologies

Keywords
   Biological processClathrin-mediated endocytosis of virus by host
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 endocytosis by host
Virus entry into host cell
   Cellular componentCapsid protein
Host cytoplasm
Host Golgi apparatus
Host membrane
Host mitochondrion
Membrane
T=4 icosahedral capsid protein
Viral envelope protein
Virion
   DomainSignal
Transmembrane
Transmembrane helix
   LigandRNA-binding
   PTMDisulfide bond
Glycoprotein
Lipoprotein
Palmitate
Phosphoprotein
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processclathrin-mediated endocytosis of virus by host cell

Inferred from electronic annotation. Source: UniProtKB-KW

fusion of virus membrane with host endosome membrane

Inferred from electronic annotation. Source: UniProtKB-KW

virion attachment to host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentT=4 icosahedral viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

host cell Golgi membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell mitochondrion

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

viral envelope

Inferred from electronic annotation. Source: UniProtKB-KW

viral nucleocapsid

Inferred from electronic annotation. Source: InterPro

virion membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 300300Capsid protein
PRO_0000041302
Signal peptide278 – 30023Not cleaved Potential
Chain301 – 582282E2 envelope glycoprotein
PRO_0000041303
Signal peptide563 – 58220Not cleaved Potential
Chain583 – 1063481E1 envelope glycoprotein
PRO_0000041304

Regions

Topological domain301 – 534234Extracellular Potential
Transmembrane535 – 55521Helical; Note=Golgi retention signal; Potential
Topological domain556 – 58227Cytoplasmic Potential
Topological domain583 – 1028446Extracellular Potential
Transmembrane1029 – 104921Helical; Note=Endoplasmic reticulum retention signal; Potential
Topological domain1050 – 106314Cytoplasmic Potential
Region30 – 6940Human C1QBP/SF2P32-binding

Sites

Site300 – 3012Cleavage; by host signal peptidase Potential
Site582 – 5832Cleavage; by host signal peptidase Potential

Amino acid modifications

Modified residue461Phosphoserine; by host Ref.17
Glycosylation6581N-linked (GlcNAc...); by host Ref.16
Glycosylation7591N-linked (GlcNAc...); by host Ref.16
Glycosylation7911N-linked (GlcNAc...); by host Ref.16
Disulfide bond590 ↔ 595 By similarity
Disulfide bond619 ↔ 824 By similarity
Disulfide bond641 ↔ 653 By similarity
Disulfide bond699 ↔ 712 By similarity
Disulfide bond758 ↔ 767 By similarity
Disulfide bond807 ↔ 817 By similarity
Disulfide bond931 ↔ 934 By similarity
Disulfide bond950 ↔ 983 By similarity

Natural variations

Natural variant2721H → R in strain: Isolate HPV77 vaccine.
Natural variant4111S → Y in strain: Isolate HPV77 vaccine.
Natural variant4121T → I in strain: Isolate HPV77 vaccine.
Natural variant4131T → A in strain: Isolate HPV77 vaccine.
Natural variant6091R → G in strain: Isolate HPV77 vaccine.

Experimental info

Mutagenesis35 – 439RRPRPPRQR → AAPAPPAQA: Complete loss of human C1QBP/SF2P32-binding. 90% loss of virus production from infected cell. Ref.18
Mutagenesis60 – 689RRRRGNRGR → AAAAGNAGA: Complete loss of human C1QBP/SF2P32-binding. 90% loss of virus production from infected cell. Ref.18
Mutagenesis1531C → S: Complete loss of Capsid dimerization. No effect on particle budding. Ref.7
Mutagenesis6581N → I: Complete loss of infectivity. Ref.16
Mutagenesis6641C → S: Prevents E1-E2 heterodimer formation, and subsequent transport of to the plasma membrane. Complete loss of fusion activity in vitro. Ref.9
Mutagenesis6751G → D: Complete loss of fusion activity in vitro. 90% loss of infectivity in vivo. No effect on virus assembly. Ref.9 Ref.13
Mutagenesis6861P → G: 99.9% loss of infectivity. No effect on virus assembly. No effect on fusion activity in vitro. Ref.9 Ref.13
Mutagenesis7591N → I: No effect on infectivity. Ref.16
Mutagenesis7911N → I: Complete loss of infectivity. Ref.16
Mutagenesis10461L → A: No effect on virus production from infected cell. Ref.10
Mutagenesis10481C → A: No effect on virus production from infected cell. Ref.10
Mutagenesis10491C → A: No effect on virus production from infected cell. Ref.10
Mutagenesis10521C → A: No effect on virus production from infected cell. Ref.10 Ref.12
Mutagenesis10531L → A: 90% loss of virus production from infected cell. Ref.10 Ref.12
Mutagenesis10541Y → A: Complete loss of virus production from infected cell. Ref.12
Mutagenesis10551Y → S: Complete loss of virus production from infected cell. Ref.12
Mutagenesis10561L → A: 90% loss of virus production from infected cell. Ref.12
Mutagenesis10571R → S: 98% loss of virus production from infected cell. Ref.12
Mutagenesis10581G → C: 98% loss of virus production from infected cell. Ref.12
Mutagenesis10591A → S: 90% loss of virus production from infected cell. Ref.12
Mutagenesis10601I → V: No effect on virus production from infected cell. Ref.12
Mutagenesis10611A → S: 90% loss of virus production from infected cell. Ref.12
Mutagenesis10621P → S: 90% loss of virus production from infected cell. Ref.12
Mutagenesis10631R → S: 98% loss of virus production from infected cell. Ref.12
Sequence conflict42 – 6928QRDSS…NRGRG → HARLQHLPEMTPAVTPEGPA PPRTGAW in CAA28880. Ref.1
Sequence conflict1751T → I in CAA28880. Ref.1
Sequence conflict445 – 47127RHGAD…PTRFG → PTALTPGAVGDLRAVHHRPV PAYPVC in CAA28880. Ref.1
Sequence conflict4851V → I in CAA28880. Ref.1
Sequence conflict562 – 57716RGAAA…LQGYN → PAPPPPSPQSSCRGTT in CAA28880. Ref.1
Sequence conflict993 – 9942RV → GH in CAA28880. Ref.1
Sequence conflict995 – 106369Missing in CAA28880. Ref.1

Secondary structure

......................................................................................................... 1063
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P08563 [UniParc].

Last modified May 30, 2006. Version 2.
Checksum: B546067276483ECB

FASTA1,063114,736
        10         20         30         40         50         60 
MASTTPITME DLQKALEAQS RALRAGLAAG ASQSRRPRPP RQRDSSTSGD DSGRDSGGPR 

        70         80         90        100        110        120 
RRRGNRGRGQ RKDWSRAPPP PEERQESRSQ TPAPKPSRAP PQQPQPPRMQ TGRGGSAPRP 

       130        140        150        160        170        180 
ELGPPTNPFQ AAVARGLRPP LHDPDTEAPT EACVTSWLWS EGEGAVFYRV DLHFTNLGTP 

       190        200        210        220        230        240 
PLDEDGRWDP ALMYNPCGPE PPAHVVRAYN QPAGDVRGVW GKGERTYAEQ DFRVGGTRWH 

       250        260        270        280        290        300 
RLLRMPVRGL DGDTAPLPPH TTERIETRSA RHPWRIRFGA PQAFLAGLLL AAVAVGTARA 

       310        320        330        340        350        360 
GLQPRADMAA PPMPPQPPRA HGQHYGHHHH QLPFLGHDGH HGGTLRVGQH HRNASDVLPG 

       370        380        390        400        410        420 
HWLQGGWGCY NLSDWHQGTH VCHTKHMDFW CVEHDRPPPA TPTSLTTAAN STTAATPATA 

       430        440        450        460        470        480 
PPPCHAGLND SCGGFLSGCG PMRLRHGADT RCGRLICGLS TTAQYPPTRF GCAMRWGLPP 

       490        500        510        520        530        540 
WELVVLTARP EDGWTCRGVP AHPGTRCPEL VSPMGRATCS PASALWLATA NALSLDHAFA 

       550        560        570        580        590        600 
AFVLLVPWVL IFMVCRRACR RRGAAAALTA VVLQGYNPPA YGEEAFTYLC TAPGCATQTP 

       610        620        630        640        650        660 
VPVRLAGVRF ESKIVDGGCF APWDLEATGA CICEIPTDVS CEGLGAWVPT APCARIWNGT 

       670        680        690        700        710        720 
QRACTFWAVN AYSSGGYAQL ASYFNPGGSY YKQYHPTACE VEPAFGHSDA ACWGFPTDTV 

       730        740        750        760        770        780 
MSVFALASYV QHPHKTVRVK FHTETRTVWQ LSVAGVSCNV TTEHPFCNTP HGQLEVQVPP 

       790        800        810        820        830        840 
DPGDLVEYIM NYTGNQQSRW GLGSPNCHGP DWASPVCQRH SPDCSRLVGA TPERPRLRLV 

       850        860        870        880        890        900 
DADDPLLRTA PGPGEVWVTP VIGSQARKCG LHIRAGPYGH ATVEMPEWIH AHTTSDPWHP 

       910        920        930        940        950        960 
PGPLGLKFKT VRPVALPRAL APPRNVRVTG CYQCGTPALV EGLAPGGGNC HLTVNGEDVG 

       970        980        990       1000       1010       1020 
AFPPGKFVTA ALLNTPPPYQ VSCGGESDRA SARVIDPAAQ SFTGVVYGTH TTAVSETRQT 

      1030       1040       1050       1060 
WAEWAAAHWW QLTLGAICAL LLAGLLACCA KCLYYLRGAI APR 

« Hide

References

[1]"Nucleotide sequence and in vitro expression of rubella virus 24S subgenomic messenger RNA encoding the structural proteins E1, E2 and C."
Clarke D.M., Loo T.W., Hui I., Chong P., Gillam S.
Nucleic Acids Res. 15:3041-3057(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Expression of rubella virus cDNA coding for the structural proteins."
Clarke D.M., Loo T.W., McDonald H., Gillam S.
Gene 65:23-30(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION.
[3]"Nucleotide sequence of the 24S subgenomic messenger RNA of a vaccine strain (HPV77) of rubella virus: comparison with a wild-type strain (M33)."
Zheng D., Dickens L., Liu T.Y., Nakhasi H.L.
Gene 82:343-349(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Isolate HPV77 vaccine.
[4]"Analysis of rubella virus E1 glycosylation mutants expressed in COS cells."
Hobman T.C., Qiu Z., Chaye H., Gillam S.
Virology 181:768-772(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION OF E1 ENVELOPE GLYCOPROTEIN.
[5]"The rubella virus E2 and E1 spike glycoproteins are targeted to the Golgi complex."
Hobman T.C., Woodward L., Farquhar M.G.
J. Cell Biol. 121:269-281(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION OF E1 AND E2 ENVELOPE GLYCOPROTEINS.
[6]"Targeting of a heterodimeric membrane protein complex to the Golgi: rubella virus E2 glycoprotein contains a transmembrane Golgi retention signal."
Hobman T.C., Woodward L., Farquhar M.G.
Mol. Biol. Cell 6:7-20(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[7]"Dimerization of rubella virus capsid protein is not required for virus particle formation."
Lee J.Y., Hwang D., Gillam S.
Virology 216:223-227(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF CYS-153.
[8]"Characterization of an endoplasmic reticulum retention signal in the rubella virus E1 glycoprotein."
Hobman T.C., Lemon H.F., Jewell K.
J. Virol. 71:7670-7680(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[9]"Effects of mutations in the rubella virus E1 glycoprotein on E1-E2 interaction and membrane fusion activity."
Yang D., Hwang D., Qiu Z., Gillam S.
J. Virol. 72:8747-8755(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF CYS-664; GLY-675 AND PRO-686.
[10]"Mutational analysis, using a full-length rubella virus cDNA clone, of rubella virus E1 transmembrane and cytoplasmic domains required for virus release."
Yao J., Gillam S.
J. Virol. 73:4622-4630(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LEU-1046; CYS-1048; CYS-1049; CYS-1052 AND LEU-1053.
[11]"Rubella virus capsid associates with host cell protein p32 and localizes to mitochondria."
Beatch M.D., Hobman T.C.
J. Virol. 74:5569-5576(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HUMAN C1QBP.
[12]"A single-amino-acid substitution of a tyrosine residue in the rubella virus E1 cytoplasmic domain blocks virus release."
Yao J., Gillam S.
J. Virol. 74:3029-3036(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF CYS-1052; LEU-1053; TYR-1054; TYR-1055; LEU-1056; ARG-1057; GLY-1058; ALA-1059; ILE-1060; ALA-1061; PRO-1062 AND ARG-1063.
[13]"Mutations in the E1 hydrophobic domain of rubella virus impair virus infectivity but not virus assembly."
Qiu Z., Yao J., Cao H., Gillam S.
J. Virol. 74:6637-6642(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLY-675 AND PRO-686.
[14]"Rubella virus capsid protein induces apoptosis in transfected RK13 cells."
Duncan R., Esmaili A., Law L.M., Bertholet S., Hough C., Hobman T.C., Nakhasi H.L.
Virology 275:20-29(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF CAPSID PROTEIN.
[15]"Rubella virus E2 signal peptide is required for perinuclear localization of capsid protein and virus assembly."
Law L.M., Duncan R., Esmaili A., Nakhasi H.L., Hobman T.C.
J. Virol. 75:1978-1983(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF CAPSID PROTEIN.
[16]"Effect of site-directed asparagine to isoleucine substitutions at the N-linked E1 glycosylation sites on rubella virus viability."
Ramanujam M., Hofmann J., Nakhasi H.L., Atreya C.D.
Virus Res. 81:151-156(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION AT ASN-658; ASN-759 AND ASN-791, MUTAGENESIS OF ASN-658; ASN-759 AND ASN-791.
[17]"Phosphorylation of rubella virus capsid regulates its RNA binding activity and virus replication."
Law L.M., Everitt J.C., Beatch M.D., Holmes C.F., Hobman T.C.
J. Virol. 77:1764-1771(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT SER-46, RNA-BINDING.
[18]"Interactions between rubella virus capsid and host protein p32 are important for virus replication."
Beatch M.D., Everitt J.C., Law L.J., Hobman T.C.
J. Virol. 79:10807-10820(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF 35-ARG--ARG-43 AND 60-ARG--ARG-68.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X05259 mRNA. Translation: CAA28880.1. Sequence problems.
M30776 Genomic RNA. Translation: AAA47421.1. Sequence problems.
PIRGNWVR3. A27505.
GNWV77. JQ0087.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4ADGX-ray2.18A/B/C583-1018[»]
4ADIX-ray1.80A/B/C583-1018[»]
4ADJX-ray1.94A/B/C583-1018[»]
4B3VX-ray1.98A/B/C583-1018[»]
4HARX-ray2.66A/B/C/D/E/F127-277[»]
4HBEX-ray2.30A/B127-277[»]
4HBOX-ray3.24A/B/C/D/E147-277[»]
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR008819. Rubella_Capsid.
IPR008820. Rubella_E1.
IPR008821. Rubella_E2.
[Graphical view]
PfamPF05750. Rubella_Capsid. 1 hit.
PF05748. Rubella_E1. 1 hit.
PF05749. Rubella_E2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLS_RUBVM
AccessionPrimary (citable) accession number: P08563
Secondary accession number(s): P21480 expand/collapse secondary AC list , Q86373, Q86374, Q86375
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: May 30, 2006
Last modified: March 19, 2014
This is version 83 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references