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9  structures 21  species 0  interactions 21  sequences 1  architecture

Family: Polyhedrin (PF00738)

Summary: Polyhedrin

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

Polyhedrin Edit Wikipedia article

Polyhedrin dodekamer, Cypovirus 1.
The crystal structure of recombinant baculovirus polyhedra.[1]
Symbol Polyhedrin
Pfam PF00738
InterPro IPR001746

Polyhedrins are proteins that form the Baculovirus occlusion bodies (also known as Polyhedra), large structures that protect the virus particles from the outside environment for extended periods until they are ingested by other susceptible insect population. The structure of polyhedrin comprises multiple beta strands, three alpha helices, and two pi helices, and are often covered in a polysaccharide coat. The polysaccharide coat confers integrity to the structure of the occlusion bodies, allowing it to remain viable in the environment for up to 40–50 years.[2]

They occur in various viruses including Nuclear polyhedrosis virus (NPV) and Granulovirus (GV). GV is singly enveloped and have one virus particle per occlusion. This is while NPVs have the potential to package multiple virus genomes in an occlusion. The occlusion bodies are usually formed in nucleus of virus infected cells approximately 2 days after the infection.


  1. ^ PDB: 2WUX​; Ji X, Sutton G, Evans G, Axford D, Owen R, Stuart DI (January 2010). "How baculovirus polyhedra fit square pegs into round holes to robustly package viruses". EMBO J. 29 (2): 505–14. doi:10.1038/emboj.2009.352. PMC 2824454Freely accessible. PMID 19959989. 
  2. ^ Rohrmann (1986). "Polyhedrin structure". J Gen Virol. 67 (8): 1499–513. doi:10.1099/0022-1317-67-8-1499. PMID 3525744. 

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.

Polyhedrin Provide feedback

These proteins are found in occlusion bodies in various viruses. The polyhedrin protein protects the virus.

This tab holds annotation information from the InterPro database.

InterPro entry IPR001746

These occlusion proteins are major components of the virus occlusion bodies, large proteinaceous structures (polyhedra) that protect the virus from the outside environment for extended periods until they are ingested by insect larvae. They occur in various viruses including the single nucleocapsid nuclear polyhedrosis viruses and granuloviruses.

Gene Ontology

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Domain organisation

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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.

Curation View help on the curation process

Seed source: Pfam-B_423 (release 2.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 3
Number in full: 21
Average length of the domain: 232.00 aa
Average identity of full alignment: 66 %
Average coverage of the sequence by the domain: 94.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 411.2 411.0
Noise cut-off 22.6 20.4
Model length: 232
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Polyhedrin 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 sequence.

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