Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
4  structures 82  species 0  interactions 296  sequences 20  architectures

Family: Gag_MA (PF01140)

Summary: Matrix protein (MA), p15

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Retroviral matrix protein". More...

Retroviral matrix protein Edit Wikipedia article

Retroviral matrix proteins are components of envelope-associated capsids of retroviruses. These proteins line the inner surface of viral envelopes and are associated with viral membranes.[1]

Matrix proteins are produced as N-terminal domains of Gag precursor polyproteins. 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 (which corresponds to the matrix protein) 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 .[2] During viral maturation, the Gag polyprotein is cleaved by the retroviral protease into several corresponding structural proteins, yielding the matrix (MA), capsid (CA), nucleocapsid (NC) proteins, and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding.

Families of retroviral matrix proteins[edit]

Gag_MA
PDB 1mn8 EBI.jpg
structure of moloney murine leukaemia virus matrix protein
Identifiers
Symbol Gag_MA
Pfam PF01140
Pfam clan CL0074
InterPro IPR000840
SCOP 1mn8
SUPERFAMILY 1mn8
OPM superfamily 44
OPM protein 1mn8

Although matrix proteins from different viruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. Typical matrix proteins of retroviruses form an alpha helical bundle structure .[3]

One family of these proteins represents matrix proteins from gamma-retroviruses, such as Moloney murine leukemia virus (MoMLV), Feline leukemia virus (FLV), and Feline sarcoma virus (FESV).[4][5] This family also includes matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome.[6]

Retro_M
PDB 1a6s EBI.jpg
m-domain from gag polyprotein of rous sarcoma virus, nmr, 20 structures
Identifiers
Symbol Retro_M
Pfam PF02813
Pfam clan CL0074
InterPro IPR004028
SCOP 1a6s
SUPERFAMILY 1a6s
OPM superfamily 44
OPM protein 1a6s

Another family represents the M domain of the Gag polyprotein found in avian retroviruses. It includes Gag polyproteins from several avian endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome .[7]

Gag_p10
PDB 2f76 EBI.jpg
solution structure of the m-pmv wild type matrix protein (p10)
Identifiers
Symbol Gag_p10
Pfam PF02337
Pfam clan CL0074
InterPro IPR003322
OPM superfamily 44
OPM protein 2lpy

Matrix proteins are also components of beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) .[8][9] This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome.[6]

Gag_p15
PDB 1hek EBI.jpg
crystal structure of equine infectious anaemia virus matrix antigen (eiav ma)
Identifiers
Symbol Gag_p15
Pfam PF08723
InterPro IPR014834
SCOP 1hek
SUPERFAMILY 1hek
OPM superfamily 44
OPM protein 1hek

References[edit]

  1. ^ Conte MR, Matthews S (July 1998). "Retroviral matrix proteins: a structural perspective". Virology 246 (2): 191–8. doi:10.1006/viro.1998.9206. PMID 9657938. 
  2. ^ Parent LJ, Cairns TM, Albert JA, Wilson CB, Wills JW, Craven RC (January 2000). "RNA dimerization defect in a Rous sarcoma virus matrix mutant". J. Virol. 74 (1): 164–72. PMC 111525. PMID 10590103. 
  3. ^ McDonnell JM, Fushman D, Cahill SM, Zhou W, Wolven A, Wilson CB, Nelle TD, Resh MD, Wills J, Cowburn D (June 1998). "Solution structure and dynamics of the bioactive retroviral M domain from Rous sarcoma virus". J. Mol. Biol. 279 (4): 921–8. doi:10.1006/jmbi.1998.1788. PMID 9642071. 
  4. ^ Riffel N, Harlos K, Iourin O, Rao Z, Kingsman A, Stuart D, Fry E (December 2002). "Atomic resolution structure of Moloney murine leukemia virus matrix protein and its relationship to other retroviral matrix proteins". Structure 10 (12): 1627–36. doi:10.1016/S0969-2126(02)00896-1. PMID 12467570. 
  5. ^ Baker SJ, Cosenza SC, Reddy EP (September 1998). "The role of v-Fgr myristoylation and the Gag domain in membrane binding and cellular transformation". Virology 249 (1): 1–11. doi:10.1006/viro.1998.9323. PMID 9740771. 
  6. ^ a b Gifford R, Tristem M (May 2003). "The evolution, distribution and diversity of endogenous retroviruses". Virus Genes 26 (3): 291–315. doi:10.1023/A:1024455415443. PMID 12876457. 
  7. ^ Borisenko L (2003). "Avian endogenous retroviruses". Folia Biol. (Praha) 49 (5): 177–82. PMID 14680291. 
  8. ^ Stansell E, Tytler E, Walter MR, Hunter E (May 2004). "An early stage of Mason-Pfizer monkey virus budding is regulated by the hydrophobicity of the Gag matrix domain core". J. Virol. 78 (10): 5023–31. PMC 400380. PMID 15113883. 
  9. ^ Poon DT, Li G, Aldovini A (March 1998). "Nucleocapsid and matrix protein contributions to selective human immunodeficiency virus type 1 genomic RNA packaging". J. Virol. 72 (3): 1983–93. PMC 109491. PMID 9499052. 

This article incorporates text from the public domain Pfam and InterPro IPR000840

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.

Matrix protein (MA), p15 Provide feedback

The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity [1].

Literature references

  1. Pozsgay JM, Beilharz MW, Wines BD, Hess AD, Pitha PM; , J Virol 1993;67:5989-5999.: The MA (p15) and p12 regions of the gag gene are sufficient for the pathogenicity of the murine AIDS virus. PUBMED:7690416 EPMC:7690416


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000840

Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes [PUBMED:9657938]. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different.

This entry represents matrix proteins from gamma-retroviruses, such as Moloney murine leukemia virus (MoMLV), Feline leukemia virus (FLV), and Feline sarcoma virus (FESV) [PUBMED:12467570, PUBMED:9740771]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [PUBMED:12876457].

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan Matrix (CL0074), which has the following description:

This clan brings together matrix proteins from a variety of retroviruses.

The clan contains the following 5 members:

Gag_MA Gag_p10 Gag_p17 Gag_p19 Retro_M

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...

View options

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
(296)
Representative proteomes NCBI
(313)
Meta
(0)
RP15
(4)
RP35
(4)
RP55
(9)
RP75
(9)
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(9)
Full
(296)
Representative proteomes NCBI
(313)
Meta
(0)
RP15
(4)
RP35
(4)
RP55
(9)
RP75
(9)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(296)
Representative proteomes NCBI
(313)
Meta
(0)
RP15
(4)
RP35
(4)
RP55
(9)
RP75
(9)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   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

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...

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_229 (release 3.0)
Previous IDs: gag_MA;
Type: Family
Author: Finn RD, Bateman A
Number in seed: 9
Number in full: 296
Average length of the domain: 123.90 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 20.54 %

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 20.8 20.8
Trusted cut-off 21.0 22.1
Noise cut-off 19.8 19.8
Model length: 129
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Gag_MA domain has been found. There are 4 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.

Loading structure mapping...