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2  structures 30  species 0  interactions 161  sequences 4  architectures

Family: Birna_VP3 (PF01767)

Summary: Birnavirus VP3 protein

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This is the Wikipedia entry entitled "Birnaviridae". More...

Birnaviridae Edit Wikipedia article

Birnaviridae
Virus classification
Group: Group III (dsRNA)
Family: Birnaviridae
Genera

Aquabirnavirus
Avibirnavirus
Blosnavirus
Entomobirnavirus

Birnavirus RNA dependent RNA polymerase (VP1)
Identifiers
Symbol Birna_RdRp
Pfam PF04197
InterPro IPR007100
Birnavirus VP2 protein
PDB 2df7 EBI.jpg
crystal structure of infectious bursal disease virus vp2 subviral particle
Identifiers
Symbol Birna_VP2
Pfam PF01766
Pfam clan CL0055
InterPro IPR002662
Birnavirus VP3 protein
Identifiers
Symbol Birna_VP3
Pfam PF01767
InterPro IPR002663
Birnavirus VP4 protein
Identifiers
Symbol Birna_VP4
Pfam PF01768
InterPro IPR002664
MEROPS S50
Birnavirus VP5 protein
Identifiers
Symbol Birna_VP5
Pfam PF03042
InterPro IPR004284

The Birnaviridae are a family of viruses, including the following genera:

The Birnaviridae are type-III viruses in the Baltimore classification, which means they have a double-stranded RNA genome. The other family of type-III viruses is the Reoviridae.

Birnaviridae proteins[edit]

The Birnaviridae genome encodes several proteins:

The Birnaviridae RNA-directed RNA polymerase (VP1), which lacks the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RNA-directed RNA polymerases.[1]

The large RNA segment, segment A, of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C) [2] that is processed into the major structural proteins of the virion: VP2, VP3 (a minor structural component of the virus), and into the putative protease VP4.[2] VP4 protein is involved in generating VP2 and VP3.[2] recombinant VP3 is more immunogenic than recombinant VP2.[3]

Infectious pancreatic necrosis virus (IPNV), a birnavirus, is an important pathogen in fish farms. Analyses of viral proteins showed that VP2 is the major structural and immunogenic polypeptide of the virus.[4][5] All neutralizing monoclonal antibodies are specific to VP2 and bind to continuous or discontinuous epitopes. The variable domain of VP2 and the 20 adjacent amino acids of the conserved C-terminal are probably the most important in inducing an immune response for the protection of animals.[4]

Non structural protein VP5 is found in RNA segment A. The function of this small viral protein is unknown. It is believed to be involved in influencing apoptosis, but studies are not completely concurring. The protein can not be found in the virion.

Viruses[edit]

The family includes a number of viruses:

Chicken proventricular necrosis virus

References[edit]

  1. ^ Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R (May 2002). "Birnavirus VP1 proteins form a distinct subgroup of RNA-dependent RNA polymerases lacking a GDD motif". Virology 296 (2): 241–50. doi:10.1006/viro.2001.1334. PMID 12069523. 
  2. ^ a b c Jagadish MN, Staton VJ, Hudson PJ, Azad AA (March 1988). "Birnavirus precursor polyprotein is processed in Escherichia coli by its own virus-encoded polypeptide". J. Virol. 62 (3): 1084–7. PMC 253673. PMID 2828658. 
  3. ^ Moon CH, Do JW, Cha SJ, Bang JD, Park MA, Yoo DJ, Lee JM, Kim HG, Chung DK, Park JW (October 2004). "Comparison of the immunogenicity of recombinant VP2 and VP3 of infectious pancreatic necrosis virus and marine birnavirus". Arch. Virol. 149 (10): 2059–68. PMID 15669113. 
  4. ^ a b Heppell J, Tarrab E, Lecomte J, Berthiaume L, Arella M (December 1995). "Strain variability and localization of important epitopes on the major structural protein (VP2) of infectious pancreatic necrosis virus". Virology 214 (1): 40–9. doi:10.1006/viro.1995.9956. PMID 8525637. 
  5. ^ Nobiron I, Galloux M, Henry C, Torhy C, Boudinot P, Lejal N, Da Costa B, Delmas B (February 2008). "Genome and polypeptides characterization of Tellina virus 1 reveals a fifth genetic cluster in the Birnaviridae family". Virology 371 (2): 350–61. doi:10.1016/j.virol.2007.09.022. PMID 17976679. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR002664

This article incorporates text from the public domain Pfam and InterPro IPR002663

This article incorporates text from the public domain Pfam and InterPro IPR004284

This article incorporates text from the public domain Pfam and InterPro IPR002662

This article incorporates text from the public domain Pfam and InterPro IPR007100

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Birnavirus VP3 protein Provide feedback

VP3 is a minor structural component of the virus. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C) [1].

Literature references

  1. Jagadish MN, Staton VJ, Hudson PJ, Azad AA; , J Virol 1988;62:1084-1087.: Birnavirus precursor polyprotein is processed in Escherichia coli by its own virus-encoded polypeptide. PUBMED:2828658 EPMC:2828658


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002663

VP3 is a minor structural component of the virus. The large RNA segment of Birnaviridae codes for a polyprotein (N-VP2-VP4-VP3-C) [PUBMED:2828658].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Alignments

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Representative proteomes NCBI
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RP55
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  Seed
(5)
Full
(161)
Representative proteomes NCBI
(176)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
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RP75
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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.

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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.

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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.

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Seed source: Pfam-B_946 (release 4.2)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 5
Number in full: 161
Average length of the domain: 219.30 aa
Average identity of full alignment: 65 %
Average coverage of the sequence by the domain: 23.46 %

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 20.8 20.8
Trusted cut-off 29.1 28.5
Noise cut-off 20.3 20.2
Model length: 243
Family (HMM) version: 11
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Species distribution

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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 Birna_VP3 domain has been found. There are 2 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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