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Protein

Structural polyprotein

Gene
N/A
Organism
Rubella virus (strain M33) (RUBV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.
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.
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.By similarity2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Clathrin-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

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyprotein
Alternative name(s):
p110
Cleaved into the following 3 chains:
Alternative name(s):
Coat protein
Short name:
C
Alternative name(s):
Spike glycoprotein E2
Alternative name(s):
Spike glycoprotein E1
OrganismiRubella virus (strain M33) (RUBV)
Taxonomic identifieri11043 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTogaviridaeRubivirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007143 Componenti: Genome

Subcellular locationi

Capsid protein :
E1 envelope glycoprotein :
E2 envelope glycoprotein :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini301 – 534ExtracellularSequence analysisAdd BLAST234
Transmembranei535 – 555Helical; Note=Golgi retention signalSequence analysisAdd BLAST21
Topological domaini556 – 582CytoplasmicSequence analysisAdd BLAST27
Topological domaini583 – 1028ExtracellularSequence analysisAdd BLAST446
Transmembranei1029 – 1049Helical; Note=Endoplasmic reticulum retention signalSequence analysisAdd BLAST21
Topological domaini1050 – 1063CytoplasmicSequence analysisAdd BLAST14

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Host Golgi apparatus, Host membrane, Host mitochondrion, Membrane, T=4 icosahedral capsid protein, Viral envelope protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi35 – 43RRPRPPRQR → AAPAPPAQA: Complete loss of human C1QBP/SF2P32-binding. 90% loss of virus production from infected cell. 1 Publication9
Mutagenesisi60 – 68RRRRGNRGR → AAAAGNAGA: Complete loss of human C1QBP/SF2P32-binding. 90% loss of virus production from infected cell. 1 Publication9
Mutagenesisi153C → S: Complete loss of Capsid dimerization. No effect on particle budding. 1 Publication1
Mutagenesisi658N → I: Complete loss of infectivity. 1 Publication1
Mutagenesisi664C → S: Prevents E1-E2 heterodimer formation, and subsequent transport of to the plasma membrane. Complete loss of fusion activity in vitro. 1 Publication1
Mutagenesisi675G → D: Complete loss of fusion activity in vitro. 90% loss of infectivity in vivo. No effect on virus assembly. 2 Publications1
Mutagenesisi686P → G: 99.9% loss of infectivity. No effect on virus assembly. No effect on fusion activity in vitro. 2 Publications1
Mutagenesisi759N → I: No effect on infectivity. 1 Publication1
Mutagenesisi791N → I: Complete loss of infectivity. 1 Publication1
Mutagenesisi1046L → A: No effect on virus production from infected cell. 1 Publication1
Mutagenesisi1048C → A: No effect on virus production from infected cell. 1 Publication1
Mutagenesisi1049C → A: No effect on virus production from infected cell. 1 Publication1
Mutagenesisi1052C → A: No effect on virus production from infected cell. 2 Publications1
Mutagenesisi1053L → A: 90% loss of virus production from infected cell. 2 Publications1
Mutagenesisi1054Y → A: Complete loss of virus production from infected cell. 1 Publication1
Mutagenesisi1055Y → S: Complete loss of virus production from infected cell. 1 Publication1
Mutagenesisi1056L → A: 90% loss of virus production from infected cell. 1 Publication1
Mutagenesisi1057R → S: 98% loss of virus production from infected cell. 1 Publication1
Mutagenesisi1058G → C: 98% loss of virus production from infected cell. 1 Publication1
Mutagenesisi1059A → S: 90% loss of virus production from infected cell. 1 Publication1
Mutagenesisi1060I → V: No effect on virus production from infected cell. 1 Publication1
Mutagenesisi1061A → S: 90% loss of virus production from infected cell. 1 Publication1
Mutagenesisi1062P → S: 90% loss of virus production from infected cell. 1 Publication1
Mutagenesisi1063R → S: 98% loss of virus production from infected cell. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000413021 – 300Capsid proteinAdd BLAST300
Signal peptidei278 – 300Not cleavedSequence analysisAdd BLAST23
ChainiPRO_0000041303301 – 582E2 envelope glycoproteinAdd BLAST282
Signal peptidei563 – 582Not cleavedSequence analysisAdd BLAST20
ChainiPRO_0000041304583 – 1063E1 envelope glycoproteinAdd BLAST481

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei46Phosphoserine; by host1 Publication1
Disulfide bondi590 ↔ 595By similarity
Disulfide bondi619 ↔ 824By similarity
Disulfide bondi641 ↔ 653By similarity
Glycosylationi658N-linked (GlcNAc...); by host1 Publication1
Disulfide bondi699 ↔ 712By similarity
Disulfide bondi758 ↔ 767By similarity
Glycosylationi759N-linked (GlcNAc...); by host1 Publication1
Glycosylationi791N-linked (GlcNAc...); by host1 Publication1
Disulfide bondi807 ↔ 817By similarity
Disulfide bondi931 ↔ 934By similarity
Disulfide bondi950 ↔ 983By similarity

Post-translational modificationi

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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei300 – 301Cleavage; by host signal peptidaseSequence analysis2
Sitei582 – 583Cleavage; by host signal peptidaseSequence analysis2

Keywords - PTMi

Disulfide bond, Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein

PTM databases

iPTMnetiP08563.

Interactioni

Subunit structurei

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.1 Publication

Protein-protein interaction databases

IntActiP08563. 35 interactors.

Structurei

Secondary structure

11063
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi151 – 160Combined sources10
Beta strandi162 – 164Combined sources3
Beta strandi167 – 176Combined sources10
Helixi190 – 193Combined sources4
Helixi203 – 209Combined sources7
Beta strandi216 – 221Combined sources6
Beta strandi227 – 234Combined sources8
Beta strandi237 – 244Combined sources8
Beta strandi585 – 589Combined sources5
Beta strandi599 – 601Combined sources3
Beta strandi603 – 621Combined sources19
Beta strandi625 – 634Combined sources10
Turni641 – 647Combined sources7
Helixi650 – 657Combined sources8
Beta strandi659 – 670Combined sources12
Beta strandi672 – 674Combined sources3
Beta strandi676 – 678Combined sources3
Helixi681 – 683Combined sources3
Helixi689 – 694Combined sources6
Beta strandi698 – 703Combined sources6
Beta strandi716 – 718Combined sources3
Beta strandi721 – 729Combined sources9
Helixi733 – 735Combined sources3
Beta strandi737 – 753Combined sources17
Beta strandi756 – 760Combined sources5
Beta strandi766 – 768Combined sources3
Beta strandi770 – 777Combined sources8
Beta strandi785 – 790Combined sources6
Beta strandi797 – 804Combined sources8
Turni807 – 813Combined sources7
Helixi815 – 817Combined sources3
Beta strandi818 – 821Combined sources4
Beta strandi824 – 826Combined sources3
Beta strandi836 – 839Combined sources4
Helixi845 – 848Combined sources4
Beta strandi855 – 862Combined sources8
Beta strandi869 – 875Combined sources7
Helixi878 – 880Combined sources3
Beta strandi881 – 883Combined sources3
Helixi885 – 892Combined sources8
Beta strandi894 – 896Combined sources3
Beta strandi904 – 910Combined sources7
Beta strandi924 – 936Combined sources13
Beta strandi938 – 944Combined sources7
Beta strandi946 – 948Combined sources3
Beta strandi950 – 954Combined sources5
Beta strandi957 – 962Combined sources6
Beta strandi964 – 971Combined sources8
Beta strandi980 – 989Combined sources10
Beta strandi991 – 995Combined sources5
Helixi997 – 1001Combined sources5
Turni1002 – 1004Combined sources3
Beta strandi1005 – 1008Combined sources4
Beta strandi1010 – 1014Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
SMRiP08563.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni30 – 69Human C1QBP/SF2P32-bindingAdd BLAST40

Domaini

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.

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Family and domain databases

InterProiIPR008819. Rubella_Capsid.
IPR008820. Rubella_E1.
IPR008821. Rubella_E2.
[Graphical view]
PfamiPF05750. Rubella_Capsid. 1 hit.
PF05748. Rubella_E1. 1 hit.
PF05749. Rubella_E2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P08563-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASTTPITME DLQKALEAQS RALRAGLAAG ASQSRRPRPP RQRDSSTSGD
60 70 80 90 100
DSGRDSGGPR RRRGNRGRGQ RKDWSRAPPP PEERQESRSQ TPAPKPSRAP
110 120 130 140 150
PQQPQPPRMQ TGRGGSAPRP ELGPPTNPFQ AAVARGLRPP LHDPDTEAPT
160 170 180 190 200
EACVTSWLWS EGEGAVFYRV DLHFTNLGTP PLDEDGRWDP ALMYNPCGPE
210 220 230 240 250
PPAHVVRAYN QPAGDVRGVW GKGERTYAEQ DFRVGGTRWH RLLRMPVRGL
260 270 280 290 300
DGDTAPLPPH TTERIETRSA RHPWRIRFGA PQAFLAGLLL AAVAVGTARA
310 320 330 340 350
GLQPRADMAA PPMPPQPPRA HGQHYGHHHH QLPFLGHDGH HGGTLRVGQH
360 370 380 390 400
HRNASDVLPG HWLQGGWGCY NLSDWHQGTH VCHTKHMDFW CVEHDRPPPA
410 420 430 440 450
TPTSLTTAAN STTAATPATA PPPCHAGLND SCGGFLSGCG PMRLRHGADT
460 470 480 490 500
RCGRLICGLS TTAQYPPTRF GCAMRWGLPP WELVVLTARP EDGWTCRGVP
510 520 530 540 550
AHPGTRCPEL VSPMGRATCS PASALWLATA NALSLDHAFA AFVLLVPWVL
560 570 580 590 600
IFMVCRRACR RRGAAAALTA VVLQGYNPPA YGEEAFTYLC TAPGCATQTP
610 620 630 640 650
VPVRLAGVRF ESKIVDGGCF APWDLEATGA CICEIPTDVS CEGLGAWVPT
660 670 680 690 700
APCARIWNGT QRACTFWAVN AYSSGGYAQL ASYFNPGGSY YKQYHPTACE
710 720 730 740 750
VEPAFGHSDA ACWGFPTDTV MSVFALASYV QHPHKTVRVK FHTETRTVWQ
760 770 780 790 800
LSVAGVSCNV TTEHPFCNTP HGQLEVQVPP DPGDLVEYIM NYTGNQQSRW
810 820 830 840 850
GLGSPNCHGP DWASPVCQRH SPDCSRLVGA TPERPRLRLV DADDPLLRTA
860 870 880 890 900
PGPGEVWVTP VIGSQARKCG LHIRAGPYGH ATVEMPEWIH AHTTSDPWHP
910 920 930 940 950
PGPLGLKFKT VRPVALPRAL APPRNVRVTG CYQCGTPALV EGLAPGGGNC
960 970 980 990 1000
HLTVNGEDVG AFPPGKFVTA ALLNTPPPYQ VSCGGESDRA SARVIDPAAQ
1010 1020 1030 1040 1050
SFTGVVYGTH TTAVSETRQT WAEWAAAHWW QLTLGAICAL LLAGLLACCA
1060
KCLYYLRGAI APR
Length:1,063
Mass (Da):114,736
Last modified:May 30, 2006 - v2
Checksum:iB546067276483ECB
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti42 – 69QRDSS…NRGRG → HARLQHLPEMTPAVTPEGPA PPRTGAW in CAA28880 (PubMed:3562245).CuratedAdd BLAST28
Sequence conflicti175T → I in CAA28880 (PubMed:3562245).Curated1
Sequence conflicti445 – 471RHGAD…PTRFG → PTALTPGAVGDLRAVHHRPV PAYPVC in CAA28880 (PubMed:3562245).CuratedAdd BLAST27
Sequence conflicti485V → I in CAA28880 (PubMed:3562245).Curated1
Sequence conflicti562 – 577RGAAA…LQGYN → PAPPPPSPQSSCRGTT in CAA28880 (PubMed:3562245).CuratedAdd BLAST16
Sequence conflicti993 – 994RV → GH in CAA28880 (PubMed:3562245).Curated2
Sequence conflicti995 – 1063Missing in CAA28880 (PubMed:3562245).CuratedAdd BLAST69

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti272H → R in strain: Isolate HPV77 vaccine. 1
Natural varianti411S → Y in strain: Isolate HPV77 vaccine. 1
Natural varianti412T → I in strain: Isolate HPV77 vaccine. 1
Natural varianti413T → A in strain: Isolate HPV77 vaccine. 1
Natural varianti609R → G in strain: Isolate HPV77 vaccine. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05259 mRNA. Translation: CAA28880.1. Sequence problems.
M30776 Genomic RNA. Translation: AAA47421.1. Sequence problems.
PIRiA27505. GNWVR3.
JQ0087. GNWV77.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05259 mRNA. Translation: CAA28880.1. Sequence problems.
M30776 Genomic RNA. Translation: AAA47421.1. Sequence problems.
PIRiA27505. GNWVR3.
JQ0087. GNWV77.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
SMRiP08563.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP08563. 35 interactors.

PTM databases

iPTMnetiP08563.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

InterProiIPR008819. Rubella_Capsid.
IPR008820. Rubella_E1.
IPR008821. Rubella_E2.
[Graphical view]
PfamiPF05750. Rubella_Capsid. 1 hit.
PF05748. Rubella_E1. 1 hit.
PF05749. Rubella_E2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLS_RUBVM
AccessioniPrimary (citable) accession number: P08563
Secondary accession number(s): P21480
, Q86373, Q86374, Q86375
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: May 30, 2006
Last modified: November 2, 2016
This is version 92 of the entry and version 2 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 togaviruses replication.

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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.