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9  structures 193  species 1  interaction 809  sequences 4  architectures

Family: Capsid_NCLDV (PF04451)

Summary: Large eukaryotic DNA virus major capsid protein

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Large eukaryotic DNA virus major capsid protein Provide feedback

This family includes the major capsid protein of iridoviruses, chlorella virus and Spodoptera ascovirus, which are all dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein [1]. In Chlorella virus PBCV-1 the major capsid protein is a glycoprotein [2]. The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, are referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV. The virions of different NCLDV have dramatically different structures. The major capsid proteins of iridoviruses and phycodnaviruses, both of which have icosahedral capsids surrounding an inner lipid membrane, showed a high level of sequence conservation. A more limited, but statistically significant sequence similarity was observed between these proteins and the major capsid protein (p72) of ASFV, which also has an icosahedral capsid. It was surprising, however, to find that all of these proteins shared a conserved domain with the poxvirus protein D13L, which is an integral virion component thought to form a scaffold for the formation of viral crescents and immature virion [3].

Literature references

  1. Webby RJ, Kalmakoff J; , Virus Res 1999;59:179-189.: Comparison of the major capsid protein genes, terminal redundancies, and DNA-DNA homologies of two New Zealand iridoviruses. PUBMED:10082389 EPMC:10082389

  2. Graves MV, Meints RH; , Virology 1992;188:198-207.: Characterization of the major capsid protein and cloning of its gene from algal virus PBCV-1. PUBMED:1566573 EPMC:1566573

  3. Iyer LM, Aravind L, Koonin EV; , J Virol. 2001;75:11720-11734.: Common origin of four diverse families of large eukaryotic DNA viruses. PUBMED:11689653 EPMC:11689653


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007542

The entry includes major capsid proteins (vp54 and vp72) found in Iridoviruses, Phycodnaviruses, Asfarviruses and Ascoviruses, which are all type II dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein [PUBMED:10082389]. The structure of vp54 has been determined from Paramecium bursaria Chlorella virus 1 (PBCV-1), a very large icosahedral virus containing an internal membrane enclosed within a glycoprotein coat. The vp54 protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. The vp54 protein forms a trimer, where the domains are arranged around a pseudo 6-fold axis. The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology [PUBMED:12411581].

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.

  Seed
(37)
Full
(809)
Representative proteomes NCBI
(474)
Meta
(1501)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(37)
Full
(809)
Representative proteomes NCBI
(474)
Meta
(1501)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(37)
Full
(809)
Representative proteomes NCBI
(474)
Meta
(1501)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download   Download  
Gzipped Download   Download           Download   Download  

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: DOMO:DM04206; Iyer L
Previous IDs: Capsid_Iridovir;
Type: Family
Author: Kerrison ND, Coggill P
Number in seed: 37
Number in full: 809
Average length of the domain: 166.00 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 55.42 %

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 26.5 25.5
Noise cut-off 19.2 23.7
Model length: 207
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Capsid_NCLDV

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 Capsid_NCLDV domain has been found. There are 9 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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