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30  structures 8  species 1  interaction 8  sequences 1  architecture

Family: Birna_RdRp (PF04197)

Summary: Birnavirus RNA dependent RNA polymerase (VP1)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Birnaviridae Edit Wikipedia article

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

Birnaviridae is a family of viruses. Salmonid fish, young sexually immature chickens, and insects serve as natural hosts. There are currently six species in this family, divided among 4 genera. Diseases associated with this family include: IPNV: infectious pancreatic necrosis in salmonid fish, causes significant losses to the aquaculture industry. chronic infection in adult, and acute viral disease in young salmonid fish.[1][2]

Birnaviridae proteins

The Birnaviridae genome encodes several proteins:

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.[3]

The large RNA segment, segment A, of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C) [4] 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.[4] VP4 protein is involved in generating VP2 and VP3.[4] recombinant VP3 is more immunogenic than recombinant VP2.[5]

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.[6][7] 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.[6]

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 in Birnaviridae are non-enveloped, with icosahedral and Single-shelled geometries, and T=13 symmetry. The diameter is around 70 nm. Genomes are linear and segmented, around 15.2.3-3kb in length. The genome codes for 5 to 6 proteins.[1]

Genus Structure Symmetry Capsid Genomic arrangement Genomic segmentation
Avibirnavirus Icosahedral T=13 Non-enveloped Linear Segmented
Aquabirnavirus Icosahedral T=13 Non-enveloped Linear Segmented
Blosnavirus Icosahedral T=13 Non-enveloped Linear Segmented
Entomobirnavirus Icosahedral T=13 Non-enveloped Linear Segmented

Life cycle

Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the double-stranded RNA virus replication model. Double-stranded rna virus transcription is the method of transcription. Salmonid fish, young sexually immature chickens, and insects serve as the natural host. Transmission routes are contact.[1]

Genus Host details Tissue tropism Entry details Release details Replication site Assembly site Transmission
Avibirnavirus Birds None Cell receptor endocytosis Budding Cytoplasm Cytoplasm Contact
Aquabirnavirus Salmonid fish None Cell receptor endocytosis Budding Cytoplasm Cytoplasm Contact
Blosnavirus Blotched snakehead fish None Unknown Budding Cytoplasm Cytoplasm Unknown
Entomobirnavirus Insects: diptera None Cell receptor endocytosis Budding Cytoplasm Cytoplasm Unknown


Group: dsRNA



  1. ^ a b c "Viral Zone". ExPASy. Retrieved 12 June 2015. 
  2. ^ a b ICTV. "Virus Taxonomy: 2014 Release". Retrieved 12 June 2015. 
  3. ^ 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): 241–250. doi:10.1006/viro.2001.1334. PMID 12069523. 
  4. ^ 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 253673Freely accessible. PMID 2828658. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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

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 RNA dependent RNA polymerase (VP1) Provide feedback

Birnaviruses are dsRNA viruses. This family corresponds to the RNA dependent RNA polymerase. This protein is also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack 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 RdRps [1].

Literature references

  1. Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R; , Virology 2002;296:241-250.: Birnavirus VP1 Proteins Form a Distinct Subgroup of RNA-Dependent RNA Polymerases Lacking a GDD Motif. PUBMED:12069523 EPMC:12069523

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007100

RNA-directed RNA polymerase (RdRp) (EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [PUBMED:2759231, PUBMED:8709232]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [PUBMED:11531403].

All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [PUBMED:9309225]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [PUBMED:10827187]. The domain organisation [PUBMED:9878607] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.

There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:

  • Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.
  • Mononegavirales (negative-strand RNA viruses with non-segmented genomes).
  • Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.
  • Birnaviridae family of dsRNA viruses.
The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:
  • All positive-strand RNA eukaryotic viruses with no DNA stage.
  • All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).
  • Reoviridae family of dsRNA viruses.

This family consists of the Birnaviridae enzymes. These proteins lack 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 [PUBMED:12069523].

Gene Ontology

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

Domain organisation

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

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Pfam Clan

This family is a member of clan RdRP (CL0027), which has the following description:

This clan represents the replicative RNA dependent RNA polymerase. from a variety of RNA viruses [1].

The clan contains the following 10 members:

Birna_RdRp Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2 Viral_RdRp_C


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Curation View help on the curation process

Seed source: Pfam-B_2204 (release 7.3)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 3
Number in full: 8
Average length of the domain: 834.20 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 92.60 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 391.9 390.7
Noise cut-off 24.6 23.7
Model length: 872
Family (HMM) version: 12
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Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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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_RdRp domain has been found. There are 30 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 sequence.

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