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Protein

Capsid protein VP1

Gene
N/A
Organism
Murine minute virus (strain MVMi) (MVM) (Murine parvovirus)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of two size variants of the capsid proteins, VP1 and VP2, which differ by the presence of an N-terminal extension in the minor protein VP1. The capsid encapsulates the genomic ssDNA. Capsid proteins are responsible for the attachment to host cell receptors. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptors also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi325 – 3251Magnesium 1By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Clathrin-mediated endocytosis of virus by host, Cytoplasmic inwards viral transport, Host-virus interaction, Microtubular inwards viral transport, Viral attachment to host cell, Viral penetration into host cytoplasm, Viral penetration into host nucleus, Viral penetration via permeabilization of host membrane, Virus endocytosis by host, Virus entry into host cell

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein VP1
Alternative name(s):
Coat protein VP1
OrganismiMurine minute virus (strain MVMi) (MVM) (Murine parvovirus)
Taxonomic identifieri10795 [NCBI]
Taxonomic lineageiVirusesssDNA virusesParvoviridaeParvovirinaeProtoparvovirus
Virus hostiMus musculus (Mouse) [TaxID: 10090]
Proteomesi
  • UP000007783 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host nucleus, T=1 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 729729Capsid protein VP1PRO_0000039417Add
BLAST

Structurei

Secondary structure

1
729
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi193 – 1975Combined sources
Beta strandi199 – 21517Combined sources
Beta strandi219 – 2224Combined sources
Beta strandi224 – 2285Combined sources
Beta strandi233 – 2386Combined sources
Beta strandi246 – 25611Combined sources
Turni262 – 2643Combined sources
Helixi267 – 27610Combined sources
Beta strandi277 – 2804Combined sources
Beta strandi285 – 30016Combined sources
Beta strandi302 – 3054Combined sources
Beta strandi307 – 3126Combined sources
Beta strandi320 – 3234Combined sources
Helixi333 – 3364Combined sources
Beta strandi351 – 3566Combined sources
Helixi384 – 3863Combined sources
Helixi392 – 3954Combined sources
Beta strandi399 – 4013Combined sources
Beta strandi406 – 4083Combined sources
Beta strandi428 – 4325Combined sources
Beta strandi442 – 4454Combined sources
Helixi453 – 4553Combined sources
Beta strandi461 – 4666Combined sources
Turni469 – 4713Combined sources
Beta strandi475 – 4795Combined sources
Beta strandi490 – 4923Combined sources
Beta strandi493 – 4964Combined sources
Turni505 – 5073Combined sources
Turni510 – 5145Combined sources
Beta strandi516 – 5183Combined sources
Beta strandi538 – 5403Combined sources
Helixi545 – 5473Combined sources
Beta strandi551 – 5533Combined sources
Beta strandi573 – 5753Combined sources
Beta strandi577 – 5793Combined sources
Turni586 – 5883Combined sources
Beta strandi605 – 6073Combined sources
Beta strandi628 – 6303Combined sources
Beta strandi638 – 6414Combined sources
Beta strandi653 – 6575Combined sources
Beta strandi663 – 67917Combined sources
Beta strandi694 – 7029Combined sources
Helixi703 – 7053Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MVMX-ray3.50A143-729[»]
1Z1CX-ray3.50A143-729[»]
2XGKX-ray4.20A143-729[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07302.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni19 – 6446Phospholipase A2-likeBy similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 1310Nuclear localization signalSequence analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi167 – 18317Gly-richAdd
BLAST

Domaini

The N-terminus of VP1 is sequestered within the mature capsid. It contains a phospholipase A2-like region and putative nuclear localization signals.

Sequence similaritiesi

Belongs to the parvoviridae capsid protein family.Curated

Family and domain databases

Gene3Di2.170.30.10. 1 hit.
InterProiIPR016184. Capsid/spike_ssDNA_virus.
IPR001403. Parvovirus_coat.
IPR013607. Parvovirus_coat_VP1_N.
[Graphical view]
PfamiPF00740. Parvo_coat. 1 hit.
PF08398. Parvo_coat_N. 1 hit.
[Graphical view]
SUPFAMiSSF88645. SSF88645. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform VP1 (identifier: P07302-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAPPAKRAKR GWVPPGYKYL GPGNSLDQGE PTNPSDAAAK EHDEAYDQYI
60 70 80 90 100
KSGKNPYLYF SAADQRFIDQ TKDAKDWGGK VGHYFFRTKR AFAPKLATDS
110 120 130 140 150
EPGTSGVSRA GKRTRPPAYI FINQARAKKK LTSSAAQQSS QTMSDGTSQP
160 170 180 190 200
DGGNAVHSAA RVERAADGPG GSGGGGSGGG GVGVSTGSYD NQTHYRFLGD
210 220 230 240 250
GWVEITALAT RLVHLNMPKS ENYCRIRVHN TTDTSVKGNM AKDDAHEQIW
260 270 280 290 300
TPWSLVDANA WGVWLQPSDW QYICNTMSQL NLVSLDQEIF NVVLKTVTEQ
310 320 330 340 350
DSGGQAIKIY NNDLTACMMV AVDSNNILPY TPAANSMETL GFYPWKPTIA
360 370 380 390 400
SPYRYYFCVD RDLSVTYENQ EGTIEHNVMG TPKGMNSQFF TIENTQQITL
410 420 430 440 450
LRTGDEFATG TYYFDTNPVK LTHTWQTNRQ LGQPPLLSTF PEADTDAGTL
460 470 480 490 500
TAQGSRHGAT QMEVNWVSEA IRTRPAQVGF CQPHNDFEAS RAGPFAAPKV
510 520 530 540 550
PADVTQGVDR EANGSVRYSY GKQHGENWAA HGPAPERYTW DETNFGSGRD
560 570 580 590 600
TRDGFIQSAP LVVPPPLNGI LTNANPIGTK NDIHFSNVFN SYGPLTAFSH
610 620 630 640 650
PSPVYPQGQI WDKELDLEHK PRLHITAPFV CKNNAPGQML VRLGPNLTDQ
660 670 680 690 700
YDPNGATLSR IVTYGTFFWK GKLTMRAKLR ANTTWNPVYQ VSVEDNGNSY
710 720
MSVTKWLPTA TGNMQSVPLI TRPVARNTY
Note: Minor splicing isoform.
Length:729
Mass (Da):80,236
Last modified:May 31, 2011 - v2
Checksum:i14F7CF9BB135717F
GO
Isoform VP2 (identifier: P07302-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-142: Missing.

Note: Major splicing isoform (approximately 70% of the molecules), produced by deletion of the initiating AUG for VP1 and downstream translation of VP2.
Show »
Length:587
Mass (Da):64,625
Checksum:i439FD2D9BC7C9782
GO

Sequence cautioni

The sequence AAA69569.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB46507.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB46508.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti155 – 1551A → G in CAB46507 (PubMed:3855242).Curated
Sequence conflicti155 – 1551A → G in CAB46508 (PubMed:3855242).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 142142Missing in isoform VP2. CuratedVSP_041134Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02481 Genomic DNA. Translation: CAB46507.1. Sequence problems.
X02481 Genomic DNA. Translation: CAB46508.1. Different initiation.
M12032 Genomic DNA. Translation: AAA69569.1. Sequence problems.
PIRiB23008. VCPVIM.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02481 Genomic DNA. Translation: CAB46507.1. Sequence problems.
X02481 Genomic DNA. Translation: CAB46508.1. Different initiation.
M12032 Genomic DNA. Translation: AAA69569.1. Sequence problems.
PIRiB23008. VCPVIM.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MVMX-ray3.50A143-729[»]
1Z1CX-ray3.50A143-729[»]
2XGKX-ray4.20A143-729[»]
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP07302.

Family and domain databases

Gene3Di2.170.30.10. 1 hit.
InterProiIPR016184. Capsid/spike_ssDNA_virus.
IPR001403. Parvovirus_coat.
IPR013607. Parvovirus_coat_VP1_N.
[Graphical view]
PfamiPF00740. Parvo_coat. 1 hit.
PF08398. Parvo_coat_N. 1 hit.
[Graphical view]
SUPFAMiSSF88645. SSF88645. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "DNA sequence of the lymphotropic variant of minute virus of mice, MVM(i), and comparison with the DNA sequence of the fibrotropic prototype strain."
    Astell C.R., Gardiner E.M., Tattersall P.
    J. Virol. 57:656-669(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "DNA sequence comparison between two tissue-specific variants of the autonomous parvovirus, minute virus of mice."
    Sahli R., McMaster G.K., Hirt B.
    Nucleic Acids Res. 13:3617-3633(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF 132-718.

Entry informationi

Entry nameiCAPSD_MUMIM
AccessioniPrimary (citable) accession number: P07302
Secondary accession number(s): Q9WMH2, Q9WMH3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: May 31, 2011
Last modified: June 8, 2016
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The capsids of autonomous parvoviruses expose a proportion of VP2 N-terminus and part of that sequence can be cleaved of to form VP3.

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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.