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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)DescriptionActionsGraphical viewLength
Metal bindingi325Magnesium 1By similarity1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000394171 – 729Capsid protein VP1Add BLAST729

Proteomic databases

PRIDEiP07302.

Structurei

Secondary structure

1729
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi193 – 197Combined sources5
Beta strandi199 – 215Combined sources17
Beta strandi219 – 222Combined sources4
Beta strandi224 – 228Combined sources5
Beta strandi233 – 238Combined sources6
Beta strandi246 – 256Combined sources11
Turni262 – 264Combined sources3
Helixi267 – 276Combined sources10
Beta strandi277 – 280Combined sources4
Beta strandi285 – 300Combined sources16
Beta strandi302 – 305Combined sources4
Beta strandi307 – 312Combined sources6
Beta strandi320 – 323Combined sources4
Helixi333 – 336Combined sources4
Beta strandi351 – 356Combined sources6
Helixi384 – 386Combined sources3
Helixi392 – 395Combined sources4
Beta strandi399 – 401Combined sources3
Beta strandi406 – 408Combined sources3
Beta strandi428 – 432Combined sources5
Beta strandi442 – 445Combined sources4
Helixi453 – 455Combined sources3
Beta strandi461 – 466Combined sources6
Turni469 – 471Combined sources3
Beta strandi475 – 479Combined sources5
Beta strandi490 – 492Combined sources3
Beta strandi493 – 496Combined sources4
Turni505 – 507Combined sources3
Turni510 – 514Combined sources5
Beta strandi516 – 518Combined sources3
Beta strandi538 – 540Combined sources3
Helixi545 – 547Combined sources3
Beta strandi551 – 553Combined sources3
Beta strandi573 – 575Combined sources3
Beta strandi577 – 579Combined sources3
Turni586 – 588Combined sources3
Beta strandi605 – 607Combined sources3
Beta strandi628 – 630Combined sources3
Beta strandi638 – 641Combined sources4
Beta strandi653 – 657Combined sources5
Beta strandi663 – 679Combined sources17
Beta strandi694 – 702Combined sources9
Helixi703 – 705Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MVMX-ray3.50A143-729[»]
1Z1CX-ray3.50A143-729[»]
2XGKX-ray4.20A143-729[»]
SMRiP07302.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07302.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni19 – 64Phospholipase A2-likeBy similarityAdd BLAST46

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi4 – 13Nuclear localization signalSequence analysis10

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi167 – 183Gly-richAdd BLAST17

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti155A → G in CAB46507 (PubMed:3855242).Curated1
Sequence conflicti155A → G in CAB46508 (PubMed:3855242).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0411341 – 142Missing in isoform VP2. CuratedAdd BLAST142

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MVMX-ray3.50A143-729[»]
1Z1CX-ray3.50A143-729[»]
2XGKX-ray4.20A143-729[»]
SMRiP07302.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP07302.

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...

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: November 30, 2016
This is version 101 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.