Summary: Tymovirus coat protein
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Tymovirus coat protein Edit Wikipedia article
physalis mottle virus: empty capsid
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.
- 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.
- Canady MA, Larson SB, Day J, McPherson A (1996). "Crystal structure of turnip yellow mosaic virus.". Nat Struct Biol 3 (9): 771–81. doi:10.1038/nsb0996-771. PMID 8784351.
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000574This 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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||viral capsid (GO:0019028)|
|Molecular function||structural molecule activity (GO:0005198)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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The clan contains a set of viral coat protein families and peptidase A6. The only known peptidase activity is an autolytic cleavage releasing a 44-residue C-terminal fragment. The reaction is very slow and only occurs within the assembled virion. There is debate whether this is actually a true peptidase. The virion with these coat or capsid proteins are icosahedral viruses containing sixty triangular coat protein units, each unit consisting of three proteins. The coat protein consists of two subdomains, an eight-stranded beta-barrel on the surface and a three-helix bundle on the inner face.
The clan contains the following 26 members:Astro_capsid_N Birna_VP2 Bromo_coat Calici_coat Calici_coat_C Capsid-VNN Carmo_coat_C Circo_capsid Como_LCP Como_SCP CRPV_capsid Cucumo_coat Dicistro_VP4 Luteo_coat Nepo_coat Nepo_coat_C Nepo_coat_N Peptidase_A21 Peptidase_A6 Pico_P1A Rhv SP2 TT_ORF1 Tymo_coat Viral_coat VP4_2
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Seed source:||Pfam-B_1429 (release 2.1)|
|Author:||Finn RD, Bateman A|
|Number in seed:||1|
|Number in full:||3|
|Average length of the domain:||167.30 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||20.52 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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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