MA - P17, Matrix protein

HIV P17 MA stabilizes the viral particle by remaining attached to the inner surface of the virion lipid bilayer after viral maturation.

Cite the resource by citing the following paper:
Doherty R et al. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology (2005), 9;2(1):18.

PDB-1TAM: HIV-1 (isolate UNKNOWN) Matrix protein - produced using SwissModel/SPDBV/POVray
[animated gif: 320x240 ]
PDB: 1TAM (HIV-1 Matrix)
SwissProt: P04591 (HIV-1 HXB2 GAG)
Chime Tutorial: not available
Los Alamos HIV structure DB: Matrix protein
EMBL: K03455 [EMBL/GenBank/DDBJ]
BioAfrica: Gag Protein Data Mining Tool


  • p17 (131 amino acids)

Cleavage site:


  • Inner surface of virion lipid bilayer
  • Cell cytoplasm
  • Cell nuclear membrane
  • Cell nucleus


  • Mediates virion assembly by targeting Gag and Gag-pol polyproteins to the plasma membrane (review Ref # 7, Ref. #8)
  • In entry, associates with complex that escorts vDNA to the nucleus (Ref. #4)
  • facilitates nuclear transport of vDNA, due to a karyophilic signal that is recognized by cellular nuclear import machinery (Ref. #5)

Additional Information:

  • MA is derived from the myristylated N-terminus of p55

Genomic Location: [TOP]

Reference Sequences:

HIV-1 (HXB2):

          10         20         30         40         50         60         70 
| | | | | | |
80 90 100 110 120 130
| | | | | |
[download in fasta format]

Length: 132 amino acids (Gag polyprotein: residues 1 - 132)
Molecular Weight: 14779 Da
Theoretical pI: 9.28

Protein Domains/Folds/Motifs: [TOP]

InterPro signature for Retroviral Matrix protein p17 - IPR000071

  • The structure of the protein consists of 5 α-helices, a short 3.10 helix, and a 3-stranded mixed β-sheet (Ref. #6)
  • The first 3 α-helices and the 3.10 helix surround the 4th α-helix, forming a globular domain capped by the β-sheet
  • The 5th (C-terminal) α-helix projects away from the β-sheet to expose the C-terminal residues
  • Basic residues, that function in membrane-binding and nuclear localization, cluster around the cationic loop that connects β-strands 1 and 2

Secondary Structure prediction:

Coiled Coil Region - ncoils:

Antigenic Sites - EMBOSS:

Predicted Motifs: Printer-friendly version

Protein kinase C:
Casein kinase II:
Tyrosine kinase:
cAMP / cGMP kinase:
Cell attachment motif:
Asp Protease motif:
Asp Prot Retro motif:
Cysteine-rich Region:
Tryptophan-rich Region:
Zinc-finger CCHC motif:
Leucine Zipper motif:

Protein-Protein Interactions: [TOP]

  • Matrix binds to karyopherins for nuclear import
  • Matrix binds to Vpr for nuclear import
  • Matrix binds to gp41 for incorporation into virion
  • Matrix binds to HO3 to enhance infectivity of released virus particles

Primary and Secondary Database Entries: [TOP]


ViralZone: HIV-1
PDB/MMDB: Search for HIV-1 & Matrix

SwissProt: P04591 (HIV-1 HXB2 GAG)
EMBL: K03455; AAB50258.1 [EMBL/GenBank/DDBJ]

InterPro: IPR000071 -
Pfam: PF00540 -
Prints: PR00234
ProDom: PD000202 (1 - 131)
SCOP: SSF47836 Retroviral matrix protein
BLOCKS: P04591
Prosite: P04591
ProtoNet: P04591
ProtoMap: P04591
Database of Interacting Proteins: P04591
ModBase: P04591
Swiss-2DPAGE: 2D gel

BioAfrica Tools:
- Gag Protein Data Mining Tool provides real-time analysis of HIV-1 Gag isolates
- HIV Structure BLAST searches for similar HIV sequences that have known structures
- HIV Proteomics Resource contains protein sequence and structure analysis tools

Reviews and References: [TOP]

Cite the resource by citing the following paper:
Doherty R et al. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology (2005), 9;2(1):18.

1 - HIV Sequence Compendium 2000
Kuiken CL, Foley B, Hahn B, Korber B, Marx PA, McCutchan F, Mellors JW, Mullins JI, Sodroski J, Wolinksy S.
Theoretical Biol. & Biophys. Group, Los Alamos Nat Lab, LA-UR 01-3860 [Read it online: Compendium]
2 - Retroviruses
Coffin JM, Hughes SH, Varmus HE.
CD-ROM ed. (2002) Cold Spring Harbor Laboratory Press [Read it online: NCBI Bookshelf]
3 - Molecular Characteristics of HIV-1 Subtype C Viruses from KwaZulu-Natal, South Africa:
Implications for Vaccine and Antiretroviral Control Strategies.
Gordon M, De Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S.
Journal of Virology 77(4): 2587-2599 (2003) [pubmed: 12551997]
4 - HIV nuclear import is governed by the phosphotyrosine-mediated binding of matrix to the
core domain of integrase.
Gallay P, Swingler S, Song J.
Cell 83: 569-576 (1995) [pubmed: 7585960]
5 - Human immunodeficiency virus infection of cells arrested in the cell cycle.
Lewis P, Hensel M, Emerman M.
EMBO J 11: 3053-3058 (1992) [pubmed: 1322294]
6 - Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.
Massiah MA, Starich MR, Paschall C, Summers MF, Christensen AM, Sundquist WI.
J Mol Biol 244: 198-223 (1994) [pubmed: 7966331]
7 - Role of HIV-1 Gag domains in viral assembly.
Scarlata S, Carter C.
Biochim Biophys Acta. 11;1614(1):62-72.(2003) [pubmed: 12873766]
8 - The structural biology of HIV assembly.
Ganser-Pornillos BK, Yeager M, Sundquist WI.
Curr Opin Struct Biol. 18(2):203-17 (2008) [pubmed: 18406133]

Page last updated by Tulio de Oliveira.