P07302 (CAPSD_MUMIM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Capsid protein VP1 Alternative name(s): Coat protein VP1
Organism	Murine minute virus (strain MVMi) (MVM) (Murine parvovirus) [Complete proteome]
Taxonomic identifier	10795 [NCBI]
Taxonomic lineage	Viruses › ssDNA viruses › Parvoviridae › Parvovirinae › Parvovirus
Virus host	Mus musculus (Mouse) [TaxID: 10090]

Protein attributes

Sequence length	729 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subcellular location	Virion By similarity. Host nucleus Potential.
Domain	The N-terminus of VP1 is sequestered within the mature capsid. It contains a phospholipase A2-like region and putative nuclear localization signals.
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.
Sequence similarities	Belongs to the parvoviridae capsid protein family.
Sequence caution	The sequence AAA69569.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence CAB46507.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence CAB46508.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Clathrin-mediated endocytosis of virus by host Cytoplasmic active transport of viral material Host-virus interaction Initiation of viral infection Microtubule-dependent active transport of viral material Viral attachment to host cell Viral penetration into host cytoplasm Viral penetration into host nucleus Viral penetration via permeabilization of host organellar membrane Virus endocytosis by host
Cellular component	Host nucleus Virion
Coding sequence diversity	Alternative splicing
Ligand	Magnesium Metal-binding
Molecular function	Capsid protein T=1 icosahedral capsid protein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform VP1 (identifier: P07302-1)

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.

Note: Minor splicing isoform.

Isoform VP2 (identifier: P07302-2)

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.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 729

729

Capsid protein VP1

PRO_0000039417

Regions

Region

19 – 64

46

Phospholipase A2-like By similarity

Motif

4 – 13

10

Nuclear localization signal Potential

Compositional bias

167 – 183

17

Gly-rich

Sites

Metal binding

325

1

Magnesium 1 By similarity

Natural variations

Alternative sequence

1 – 142

142

Missing in isoform VP2.

VSP_041134

Experimental info

Sequence conflict

155

1

A → G in CAB46507. Ref.2

Sequence conflict

155

1

A → G in CAB46508. Ref.2

Secondary structure

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729

Helix Strand Turn

Details...

Beta strand

182 – 186

5

Beta strand

192 – 196

5

Beta strand

200 – 203

4

Beta strand

213 – 217

5

Beta strand

222 – 224

3

Beta strand

235 – 245

11

Helix

256 – 265

10

Beta strand

266 – 269

4

Beta strand

274 – 289

16

Beta strand

297 – 301

5

Beta strand

309 – 311

3

Helix

322 – 325

4

Beta strand

340 – 345

6

Helix

381 – 384

4

Beta strand

431 – 434

4

Beta strand

450 – 455

6

Turn

458 – 460

3

Beta strand

464 – 466

3

Beta strand

562 – 564

3

Turn

575 – 577

3

Beta strand

628 – 630

3

Beta strand

655 – 659

5

Beta strand

661 – 666

6

Beta strand

689 – 691

3

Helix

692 – 694

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform VP1 [UniParc]. Last modified May 31, 2011. Version 2. Checksum: 14F7CF9BB135717F	FASTA	729	80,236
	10 20 30 40 50 60 MAPPAKRAKR GWVPPGYKYL GPGNSLDQGE PTNPSDAAAK EHDEAYDQYI KSGKNPYLYF 70 80 90 100 110 120 SAADQRFIDQ TKDAKDWGGK VGHYFFRTKR AFAPKLATDS EPGTSGVSRA GKRTRPPAYI 130 140 150 160 170 180 FINQARAKKK LTSSAAQQSS QTMSDGTSQP DGGNAVHSAA RVERAADGPG GSGGGGSGGG 190 200 210 220 230 240 GVGVSTGSYD NQTHYRFLGD GWVEITALAT RLVHLNMPKS ENYCRIRVHN TTDTSVKGNM 250 260 270 280 290 300 AKDDAHEQIW TPWSLVDANA WGVWLQPSDW QYICNTMSQL NLVSLDQEIF NVVLKTVTEQ 310 320 330 340 350 360 DSGGQAIKIY NNDLTACMMV AVDSNNILPY TPAANSMETL GFYPWKPTIA SPYRYYFCVD 370 380 390 400 410 420 RDLSVTYENQ EGTIEHNVMG TPKGMNSQFF TIENTQQITL LRTGDEFATG TYYFDTNPVK 430 440 450 460 470 480 LTHTWQTNRQ LGQPPLLSTF PEADTDAGTL TAQGSRHGAT QMEVNWVSEA IRTRPAQVGF 490 500 510 520 530 540 CQPHNDFEAS RAGPFAAPKV PADVTQGVDR EANGSVRYSY GKQHGENWAA HGPAPERYTW 550 560 570 580 590 600 DETNFGSGRD TRDGFIQSAP LVVPPPLNGI LTNANPIGTK NDIHFSNVFN SYGPLTAFSH 610 620 630 640 650 660 PSPVYPQGQI WDKELDLEHK PRLHITAPFV CKNNAPGQML VRLGPNLTDQ YDPNGATLSR 670 680 690 700 710 720 IVTYGTFFWK GKLTMRAKLR ANTTWNPVYQ VSVEDNGNSY MSVTKWLPTA TGNMQSVPLI TRPVARNTY
	Isoform VP2 [UniParc]. Checksum: 439FD2D9BC7C9782	FASTA	587	64,625
	10 20 30 40 50 60 MSDGTSQPDG GNAVHSAARV ERAADGPGGS GGGGSGGGGV GVSTGSYDNQ THYRFLGDGW 70 80 90 100 110 120 VEITALATRL VHLNMPKSEN YCRIRVHNTT DTSVKGNMAK DDAHEQIWTP WSLVDANAWG 130 140 150 160 170 180 VWLQPSDWQY ICNTMSQLNL VSLDQEIFNV VLKTVTEQDS GGQAIKIYNN DLTACMMVAV 190 200 210 220 230 240 DSNNILPYTP AANSMETLGF YPWKPTIASP YRYYFCVDRD LSVTYENQEG TIEHNVMGTP 250 260 270 280 290 300 KGMNSQFFTI ENTQQITLLR TGDEFATGTY YFDTNPVKLT HTWQTNRQLG QPPLLSTFPE 310 320 330 340 350 360 ADTDAGTLTA QGSRHGATQM EVNWVSEAIR TRPAQVGFCQ PHNDFEASRA GPFAAPKVPA 370 380 390 400 410 420 DVTQGVDREA NGSVRYSYGK QHGENWAAHG PAPERYTWDE TNFGSGRDTR DGFIQSAPLV 430 440 450 460 470 480 VPPPLNGILT NANPIGTKND IHFSNVFNSY GPLTAFSHPS PVYPQGQIWD KELDLEHKPR 490 500 510 520 530 540 LHITAPFVCK NNAPGQMLVR LGPNLTDQYD PNGATLSRIV TYGTFFWKGK LTMRAKLRAN 550 560 570 580 TTWNPVYQVS VEDNGNSYMS VTKWLPTATG NMQSVPLITR PVARNTY

References

[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: 3502703] [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: 3855242] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Structure determination of Minute virus of mice." Llamas-Saiz A.L., Agbandje-Mckenna M., Wikoff W.R., Bratton J., Tattersall P., Rossmann M.G. Acta Crystallogr. D 53:93-100(1997) [PubMed: 15299974] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF 132-718.
+	Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02481 Genomic DNA. Translation: CAB46507.1. Sequence problems.
X02481 Genomic DNA. Translation: CAB46508.1. Different initiation.
M12032 Genomic DNA. Translation: AAA69569.1. Sequence problems.

PIR

VCPVIM. B23008.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1MVM	X-ray	3.50	A	143-729	[»]
1Z1C	X-ray	3.50	A	143-718	[»]
2XGK	X-ray	4.20	A/B	143-729	[»]

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR016184. Capsid/spike_ssDNA_virus.
IPR001403. Parvovirus_coat.
IPR013607. Parvovirus_coat_VP1_N.
[Graphical view]

Gene3D

G3DSA:2.170.30.10. Parvo_coat. 1 hit.

Pfam

PF00740. Parvo_coat. 1 hit.
PF08398. Parvo_coat_N. 1 hit.
[Graphical view]

SUPFAM

SSF88645. Capsid/spike_ssDNA_virus. 1 hit.

ProtoNet

Search...

Entry information

Entry name

CAPSD_MUMIM

Accession

Primary (citable) accession number: P07302
Secondary accession number(s): Q9WMH2, Q9WMH3

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	May 31, 2011
Last modified:	September 21, 2011
This is version 75 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program