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27  structures 6  species 0  interactions 6  sequences 2  architectures

Family: Tymo_coat (PF00983)

Summary: Tymovirus coat protein

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This is the Wikipedia entry entitled "Tymovirus coat protein". More...

Tymovirus coat protein Edit Wikipedia article

PDB 1e57 EBI.jpg
physalis mottle virus: empty capsid
Symbol Tymo_coat
Pfam PF00983
Pfam clan CL0055
InterPro IPR000574
SCOP 1auy

In molecular biology, the Tymovirus coat protein refers to the protein coat of a virus order, named Tymovirales. More specifically this protein signature is found only in coat proteins from the related tymoviruses. The coat protein (CP) is also known as the virion protein. The virus coat is composed of 180 copies of the coat protein arranged in an icosahedral shell.


Fundamentally, the viral coat protein functions as protection for the genetic material inside the virus, and as an aid to infecting the host cell with virus DNA. Essentially, the coat protein (CP) is a link between the genetic material and infecting the host. Since the genetic material in the virus consists of RNA the coat protein contains RNA binding sites. Additionally, the coat protein contains conserved histadine amino acid residues which help the virus to spread.[1]


There are three subunits named, A, B and C. It contains a beta-jelly roll motif which consists of 9 beta-strands.[2]


  1. ^ Bink HH, Pleij CW (2002). "RNA-protein interactions in spherical viruses.". Arch Virol. 147 (12): 2261–79. PMID 12491096. doi:10.1007/s00705-002-0891-6. 
  2. ^ Canady MA, Larson SB, Day J, McPherson A (1996). "Crystal structure of turnip yellow mosaic virus.". Nat Struct Biol. 3 (9): 771–81. PMID 8784351. doi:10.1038/nsb0996-771. 

This article incorporates text from the public domain Pfam and InterPro IPR000574

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.

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Literature references

  1. Srifah P, Keese P, Shukla D, Gibbs A; , J Gen Virol 1990;71:3085-3088.: The primary structure of the virion protein gene and encoded protein of erysimum latent tymovirus. PUBMED:2273397 EPMC:2273397

  2. Canady MA, Larson SB, Day J, McPherson A; , Nat Struct Biol 1996;3:771-781.: Crystal structure of turnip yellow mosaic virus. PUBMED:8784351 EPMC:8784351

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000574

This signature is found in coat proteins from the related tymoviruses. The coat protein is also known as the virion protein. The virus coat is composed of 180 copies of the coat protein arranged in an icosahedral shell.

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

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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

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Seed source: Pfam-B_1429 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 3
Number in full: 6
Average length of the domain: 176.70 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 33.39 %

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 84.6 84.2
Noise cut-off 20.7 20.5
Model length: 179
Family (HMM) version: 21
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 Tymo_coat domain has been found. There are 27 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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