Summary: Retroviral M domain
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Retroviral M domain Provide feedback
Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.
McDonnell JM, Fushman D, Cahill SM, Zhou W, Wolven A, Wilson CB, Nelle TD, Resh MD, Wills J, Cowburn D , J Mol Biol 1998;279:921-928.: Solution structure and dynamics of the bioactive retroviral M domain from Rous sarcoma virus. PUBMED:9642071 EPMC:9642071
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This tab holds annotation information from the InterPro database.
InterPro entry IPR004028
The Gag polyprotein directs the assembly and release of virus particles from infected cells. The Gag polyprotein has three domains required for activity: an N-terminal membrane-binding (M) domain that directs Gag to the plasma membrane, an interaction (I) domain involved in Gag aggregation, and a late assembly (L) domain that mediates the budding process [PUBMED:10590103]. During viral maturation, the Gag polyprotein is then cleaved into major structural proteins by the viral protease, yielding the matrix, capsid, nucleoprotein, and some smaller peptides. In Rous sarcoma virus (RSV), the M domain consists of the first 85 residues of the matrix protein. However, unlike other Gag polyproteins, the M domain of RSV Gag is not myristylated, but retains full activity [PUBMED:11070020].This domain forms an alpha helical bundle structure [PUBMED:9642071].
This entry represents the M domain of the Gag polyprotein found in avian retroviruses. This entry also identifies Gag polyproteins from several avian endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [PUBMED:14680291].
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||3|
|Number in full:||206|
|Average length of the domain:||81.30 aa|
|Average identity of full alignment:||90 %|
|Average coverage of the sequence by the domain:||16.63 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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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 Retro_M domain has been found. There are 1 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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