Retroviral matrix protein

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), and 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]

Protein family

Gag_MA

structure of moloney murine leukaemia virus matrix protein

Identifiers
Symbol| Gag_MA
Pfam| PF01140
Pfam clan| CL0074
InterPro| IPR000840
SCOP2| 1mn8 / SCOPe / SUPFAM
OPM superfamily| 42
OPM protein| 1mn8
| Available protein structures:

Pfam  | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

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 gammaretroviruses, 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]

Protein family

Retro_M

m-domain from gag polyprotein of rous sarcoma virus, nmr, 20 structures

Identifiers
Symbol| Retro_M
Pfam| PF02813
Pfam clan| CL0074
InterPro| IPR004028
SCOP2| 1a6s / SCOPe / SUPFAM
OPM superfamily| 42
OPM protein| 1a6s
| Available protein structures:

Pfam  | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

Another family represents the M domain of the Gag polyprotein found in avian retroviruses. It includes Gag polyproteins from several avian endogenous retroviruses.[7]

Protein family

Gag_p10

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
| Available protein structures:

Pfam  | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

Matrix proteins are also components of beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) and mouse mammary tumor virus (MMTV) .[8][9] This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses.[6]

Protein family

Gag_p15

crystal structure of equine infectious anaemia virus matrix antigen (eiav ma)

Identifiers
Symbol| Gag_p15
Pfam| PF08723
InterPro| IPR014834
SCOP2| 1hek / SCOPe / SUPFAM
OPM superfamily| 44
OPM protein| 1hek
| Available protein structures:

Pfam  | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

## 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\. doi:10.1128/jvi.74.1.164-172.2000. 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. S2CID 34639116.
7. ^ Borisenko L (2003). "Avian endogenous retroviruses". Folia Biol. (Praha). 49 (5): 177–82\. doi:10.14712/fb2003049050177. 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\. doi:10.1128/jvi.78.10.5023-5031.2004. 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\. doi:10.1128/JVI.72.3.1983-1993.1998. PMC 109491. PMID 9499052.

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

* v
* t
* e

Viral proteins (early and late)

DNA|

| linear ds-DNA
(Duplodnaviria,
Varidnaviria)|

| Herpes simplex|

| VSPs:|

| capsid:|

* HHV capsid portal protein
* Herpesvirus glycoprotein B

|

VNPs:|

* vmw65
* ICP8
* ICP34.5
* ICP47

Vaccinia|

| VNPs:|

* B13R

|

Adenoviridae|

| VNPs:|

* E1A
* E1B

|

circular ds-DNA
(Duplodnaviria,
Varidnaviria?)|

| Epstein–Barr|

| VSPs:|

* LMP-1
* LMP-2

|

VNPs:|

* EBNA-1
* EBNA-2
* EBNA-3

ncRNA:|

* EBER

Baculoviridae|

| VNPs:|

* Early 35 kDa protein

|

other
(Riboviria,
Monodnaviria)|

| Polyomaviridae
(SV40, MPyV, MCPyV, HaPyV)
(non-enveloped circular ds-DNA)|

| VSPs:|

| capsid:|

* VP1
* VP2 and VP3

|

VNPs:|

| oncoprotein:|

* STag
* MTag
* LTag (SV40 Tag)

|

* Agnoprotein

Hepatitis B
(circular partially ds-DNA)|

| VSPs:|

* HBsAg
* HBcAg

* HBeAg

|

VNPs:|

* HBx
* Hepatitis B virus DNA polymerase

RNA|

| ds-RNA
(Riboviria)|

| Rotavirus
(Duplornaviricota)|

| VNPs:|

* NSP1
* NSP2
* NSP3
* NSP4
* NSP5
* NSP6

|

Rhinov., Polio, Hep A,
etc. (Pisuviricota)|

| VNPs:|

* VPg

|

ss-RNA
positive-sense
(Riboviria)|

| Hepatitis C
(Kitrinoviricota)|

| VSPs:|

* viral envelope
* E1
* E2

|

VNPs:|

* P7
* NS2
* NS3
* NS4A
* NS4B
* NS5A
* NS5B

SARS-CoV-2
(Pisuviricota)|

| VSPs:|

* viral envelope
* Spike
* Envelope
* Membrane
* Nucleocapsid

|

VNPs:|

* ORF1ab
* 3C-like protease (NS5)
* ORF3a
* ORF3b
* ORF3c
* ORF3d
* ORF6
* ORF7a
* ORF7b
* ORF8
* ORF9b

ss-RNA
negative-sense
(Negarnaviricota)|

| Influenza virus|

| VSPs:|

| capsid:|

* matrix protein
* M1 protein
* viral envelope
* M2 protein

|

glycoprotein:|

* Influenza hemagglutinin
* Neuraminidase
* HA-tag

VNPs:|

* NS1

Parainfluenza|

| VSPs:|

| glycoprotein:|

* Parainfluenza hemagglutinin-neuraminidase

|

Mumps|

| VSPs:|

| glycoprotein:|

* Mumps hemagglutinin-neuraminidase

|

Measles|

| VSPs:|

| glycoprotein:|

* Measles hemagglutinin

|

RSV|

| VSPs:|

| glycoprotein:|

* Respiratory syncytial virus G protein

|

Zaire ebolavirus|

| VSPs:|

| capsid:|

* matrix protein
* VP40
* VP24

|

Indiana vesiculovirus|

| VSPs:|

| capsid:|

* matrix protein
* Vesiculovirus matrix proteins

|

RT|

| Structure and genome of HIV|

| VSPs:|

* gag
* p24
* pol
* Integrase
* Reverse transcriptase
* HIV-1 protease
* env
* gp120
* gp41

|

VRAPs:|

* transactivators
* Tat
* Rev
* Vpr
* Nef
* Vif
* Vpu or Vpx

Multiple

*     * Rous sarcoma virus
* murine leukemia virus

| Fusion protein|

| oncoprotein:|

* Gag-onc fusion protein

|

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