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22  structures 65  species 2  interactions 191  sequences 1  architecture

Family: Orbi_VP7 (PF00897)

Summary: Orbivirus inner capsid protein VP7

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Orbivirus inner capsid protein VP7 Provide feedback

In BTV, 260 trimers of VP7 are found in the core. The major proteins of the core are VP7 and VP3. VP7 forms an outer layer around VP3 [1].

Literature references

  1. Basak AK, Grimes JM, Gouet P, Roy P, Stuart DI; , Structure 1997;5:871-883.: Structures of orbivirus VP7: implications for the role of this protein in the viral life cycle. PUBMED:9261081 EPMC:9261081


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001803

Bluetongue virus is a representative of the Orbivirus genus of the Reoviridae [PUBMED:7816101]. Orbiviruses infect mammalian hosts through insect vectors, causing economically-important diseases of domesticated animals [PUBMED:7816101]. They possess a segmented, double-stranded RNA genome within a capsid that comprises four major polypeptides, designated VP2, VP3, VP5 and VP7. On entering a target cell, an outer layer, formed from VP2 and VP5, is removed, leaving an intact core within the cell [PUBMED:7816101]. The core, which is 70nm across, contains 780 copies of VP7, which together form 260 trimeric 'bristly' capsomeres clothing an inner scaffold constructed from VP3 [PUBMED:7816101].

The 3D structure of VP7 reveals two domains, one a beta-sandwich, the other a bundle of alpha-helices, and a short C-terminal arm, which is thought to unite trimers during capsid formation [PUBMED:7816101]. A concentration of methionine residues at the core of the molecule could provide plasticity, relieving structural mismatches during assembly [PUBMED:7816101].

The 3D structure of baculovirus-expressed core protein VP7 of African horse sickness virus 4 (AHSV-4) has been determined to 2.3A resolution [PUBMED:8648715]. During crystallisation, the two-domain protein is cleaved, leaving only the top domain, in a manner reminiscent of BTV VP7; this suggests that connections between top and bottom domains are relatively weak for these two distinct orbiviruses [PUBMED:8648715]. The top domains of both BTV and AHSV VP7 are trimeric and structurally very similar. Electron density maps indicate an extra density feature along their molecular 3-fold axes, probably the result of an unidentified ion [PUBMED:8648715]. The characteristics of the molecular surface indicate the possibility of attachment to the cell via attachment of an Arg-Gly-Asp (RGD) motif in the top domain of VP7 to a cellular integrin for both of these orbiviruses [PUBMED:8648715].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(7)
Full
(191)
Representative proteomes NCBI
(159)
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  Seed
(7)
Full
(191)
Representative proteomes NCBI
(159)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(7)
Full
(191)
Representative proteomes NCBI
(159)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1523 (release 2.1)
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 7
Number in full: 191
Average length of the domain: 303.00 aa
Average identity of full alignment: 60 %
Average coverage of the sequence by the domain: 99.57 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 48.6 43.3
Noise cut-off 18.9 18.8
Model length: 350
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Orbi_VP7 Orbi_VP3

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Orbi_VP7 domain has been found. There are 22 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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