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27  structures 51  species 1  interaction 153  sequences 4  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

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

Function[edit]

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]

Structure[edit]

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

References[edit]

  1. ^ Bink HH, Pleij CW (2002). "RNA-protein interactions in spherical viruses.". Arch Virol 147 (12): 2261–79. doi:10.1007/s00705-002-0891-6. PMID 12491096. 
  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. 

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

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
(9)
Full
(153)
Representative proteomes NCBI
(158)
Meta
(0)
RP15
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RP35
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RP55
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RP75
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  Seed
(9)
Full
(153)
Representative proteomes NCBI
(158)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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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
(9)
Full
(153)
Representative proteomes NCBI
(158)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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Gzipped 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

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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: Pfam-B_1429 (release 2.1)
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 9
Number in full: 153
Average length of the domain: 167.60 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 41.30 %

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 19.0 19.0
Trusted cut-off 20.1 26.2
Noise cut-off 17.9 17.6
Model length: 172
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Tymo_coat

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 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 seqence.

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