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P17465 - VP4_ROTBN

UniProt

P17465 - VP4_ROTBN

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Protein

Outer capsid protein VP4

Gene
N/A
Organism
Rotavirus A (strain Cow/United States/NCDV-Lincoln/1969 G6-P6[1]-I2-R2-C2-M2-Ax-N2-T6-E2-Hx) (RV-A) (Rotavirus A (strain Nebraska calf diarrhea virus))
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. Rotavirus entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. According to the considered strain, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1 (By similarity).By similarity
Outer capsid protein VP5*: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment (By similarity).By similarity
VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei231 – 2322CleavageBy similarity
Sitei247 – 2482CleavageBy similarity

GO - Biological processi

  1. permeabilization of host organelle membrane involved in viral entry into host cell Source: UniProtKB-KW
  2. virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hemagglutinin

Keywords - Biological processi

Host-virus interaction, Viral attachment to host cell, Viral penetration into host cytoplasm, Viral penetration via permeabilization of host membrane, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Recommended name:
Outer capsid protein VP4
Alternative name(s):
Hemagglutinin
Cleaved into the following 2 chains:
Outer capsid protein VP8*
Outer capsid protein VP5*
OrganismiRotavirus A (strain Cow/United States/NCDV-Lincoln/1969 G6-P6[1]-I2-R2-C2-M2-Ax-N2-T6-E2-Hx) (RV-A) (Rotavirus A (strain Nebraska calf diarrhea virus))
Taxonomic identifieri36439 [NCBI]
Taxonomic lineageiViruses › dsRNA viruses › Reoviridae › Sedoreovirinae › Rotavirus › Rotavirus A ›
Virus hostiBos taurus (Bovine) [TaxID: 9913]

Subcellular locationi

Chain Outer capsid protein VP4 : Virion By similarity. Host rough endoplasmic reticulum Curated
Note: Immature double-layered particles assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum, acquiring during this process a transient lipid membrane that is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the non-structural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles (By similarity).By similarity
Chain Outer capsid protein VP8* : Virion
Note: Outer capsid protein.By similarity
Chain Outer capsid protein VP5* : Virion
Note: Outer capsid protein.By similarity

GO - Cellular componenti

  1. host cell rough endoplasmic reticulum Source: UniProtKB-SubCell
  2. viral outer capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host endoplasmic reticulum, Outer capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 775775Outer capsid protein VP4PRO_0000041123Add
BLAST
Chaini1 – 231231Outer capsid protein VP8*Sequence AnalysisPRO_0000041124Add
BLAST
Chaini248 – 775528Outer capsid protein VP5*Sequence AnalysisPRO_0000041125Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi56 – 561N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi97 – 971N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi132 – 1321N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi151 – 1511N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi183 – 1831N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi198 – 1981N-linked (GlcNAc...); by hostSequence Analysis
Disulfide bondi318 ↔ 380Sequence Analysis
Glycosylationi456 – 4561N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi507 – 5071N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi596 – 5961N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi602 – 6021N-linked (GlcNAc...); by hostSequence Analysis

Post-translational modificationi

Proteolytic cleavage by trypsin results in activation of VP4 functions and greatly increases infectivity. The penetration into the host cell is dependent on trypsin treatment of VP4. It produces two peptides, VP5* and VP8* that remain associated with the virion (By similarity).By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

VP4 is a homotrimer (Potential). VP4 adopts a dimeric appearance above the capsid surface, while forming a trimeric base anchored inside the capsid layer. Only hints of the third molecule are observed above the capsid surface. It probably performs a series of molecular rearrangements during viral entry. Prior to trypsin cleavage, it is flexible. The priming trypsin cleavage triggers its rearrangement into rigid spikes with approximate two-fold symmetry of their protruding parts. After an unknown second triggering event, cleaved VP4 may undergo another rearrangement, in which two VP5* subunits fold back on themselves and join a third subunit to form a tightly associated trimer, shaped like a folded umbrella. VP5* is a homotrimer (Potential). The trimer is coiled-coil stabilized by its C-terminus, however, its N-terminus, known as antigen domain or "body", seems to be flexible allowing it to self-associate either as a dimer or a trimer. The two- to three-fold reorganization and fold-back of VP5* may be linked to membrane penetration, by exposing its hydrophobic region. Interacts with host ITGA2 (via ITAG2 I-domain); this interaction occurs when ITGA2 is part of the integrin heterodimer ITGA2/ITGB1. Interacts with host integrin heterodimer ITGA4/ITGB1 and ITGA4/ITGB7 (By similarity).By similarityCurated

Structurei

3D structure databases

ProteinModelPortaliP17465.
SMRiP17465. Positions 64-224, 253-522.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni248 – 480233Antigen domainBy similarityAdd
BLAST
Regioni308 – 3103DGE motif; interaction with ITGA2/ITGB1 heterodimerBy similarity
Regioni389 – 40921Hydrophobic; possible role in virus entry into host cellSequence AnalysisAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili484 – 51835Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi560 – 61657Ser-richAdd
BLAST

Sequence similaritiesi

Belongs to the rotavirus VP4 family.Curated

Keywords - Domaini

Coiled coil

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR013320. ConA-like_dom.
IPR000416. Haemagglutinin_VP4.
[Graphical view]
PfamiPF00426. VP4_haemagglut. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P17465-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MASLIYRQLL TNSYTVELSD EIQEIGSTKT QDVTVNPGPF AQTNYAPVNW 
        60         70         80         90        100
GPGETNDSTT VEPVLDGPYQ PTTFNPPVSY WMLLAPTNAG VVVEGTNNTN 
       110        120        130        140        150
RWLATILIEP NVQQVERTYT LFGQQVQVTV SNDSQTKWKF VDLSKQTQDG 
       160        170        180        190        200
NYSQHGSLLS TPKLYGVMKH GGKIYTYNGE TPNATTGYYS TTNFDTVNMT 
       210        220        230        240        250
AYCDFYIIPL AQEAKCTEYI NNGLPPIQNT RNIVPVSIVS RNIVYTRAQP 
       260        270        280        290        300
NQDIVVSKTS LWKEMQYNRD IVIRFKFANS IIKSGGLGYK WSEVSFKPAN 
       310        320        330        340        350
YQYTYTRDGE EVTAHTTCSV NGINDFNYNG GSLPTDFVIS KYEVIKENSF 
       360        370        380        390        400
VYIDYWDDSQ AFRNMVNVRS LAADLNSVMC TGGDYSFALP VGNYPVMTGG 
       410        420        430        440        450
AVSLHSAGVT LSTQFTDFVS LNSLRFRFRL SVEEPPFSIL RTRVSGLYGL 
       460        470        480        490        500
PAARPNNSQE YYEIAGRFSL ISLVPSNDDY QTPIINSVTV RQDLERQLGE 
       510        520        530        540        550
LRDEFNNLSQ QIAMSQLIDL ALLPLDMFSM FSGIKSTIDA AKSMATNVMK 
       560        570        580        590        600
RFKKSSLANS VSTLTNSLSD AASSISRSAS VRSVSSTASA WTEVSNITSD 
       610        620        630        640        650
INVTTSSIST QTSTISRRLR LKEMATQTDG MNFDDISAAV LKTKIDKSTQ 
       660        670        680        690        700
LNTNTLPEIV TEASEKFIPN RAYRVKDDEV LEASTDGKYF AYKVETFEEI 
       710        720        730        740        750
PFDVQKFADL VTDSPVISAI IDFKTLKNLN DNYGISRQQA LNLLRSDPRV 
       760        770 
LREFINQDNP IIRNRIESLI MQCRL
Length:775
Mass (Da):86,549
Last modified:August 1, 1990 - v1
Checksum:iF5D28332747FD9AB
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti676 – 6761K → IK in BAC85485. 1 PublicationCurated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB119636 Genomic RNA. Translation: BAC85485.1.
PIRiC31159. VPXRT2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB119636 Genomic RNA. Translation: BAC85485.1.
PIRiC31159. VPXRT2.

3D structure databases

ProteinModelPortaliP17465.
SMRiP17465. Positions 64-224, 253-522.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR013320. ConA-like_dom.
IPR000416. Haemagglutinin_VP4.
[Graphical view]
PfamiPF00426. VP4_haemagglut. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Comparative analysis of the VP3 gene of divergent strains of the rotaviruses simian SA11 and bovine Nebraska calf diarrhea virus."
    Nishikawa K., Taniguchi K., Torres A., Hoshino Y., Green K.Y., Kapikian A.Z., Chanock R.M., Gorziglia M.
    J. Virol. 62:4022-4026(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "VP4 gene of bovine rotavirus."
    Homma S., Hoshino Y.
    Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiVP4_ROTBN
AccessioniPrimary (citable) accession number: P17465
Secondary accession number(s): Q75Z90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: January 7, 2015
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

In group A rotaviruses, VP4 defines the P serotype.
This strain has been shown to be sialic acid-dependent, and integrin-dependent in cell culture conditions.

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.