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.

PDB-1TAM: HIV-1 (isolate UNKNOWN) Matrix protein - produced using SwissModel/SPDBV/POVray

Key web links:
ViralZone: HIV-1, HIV replication cycle, HIV resource
PDB: 1TAM (HIV-1 Matrix)
UniProt: P04591 (HIV-1 HXB2 GAG)
Chime Tutorial: not available
HIV-1/Human Protein Interaction DB: HIV-1 Gag
Los Alamos HIV structure DB: Matrix protein
EMBL: K03455 [EMBL/GenBank/DDBJ]


  • p17 (131 amino acids)

Cleavage sites:


  • Mediates virion assembly by targeting Gag and Gag-pol polyproteins to the plasma membrane .
  • Incorporates Env into budding virions .
  • Displays nucleic-acid-binding ability for possible prevention of premature Gag binding to intracellular membranes prior to delivery to the plasma membrane .
  • Might be involved in the nuclear import of the pre-integration complex (PIC) .


  • Inner surface of virion lipid bilayer
  • Cell cytoplasm
  • Cell nucleus (as part of the preintegration complex)
  • Late endosomes/multivesicular bodies
  • Plasma membrane

Additional Information:

  • Late timing of expression.
  • MA is derived from the myristylated N-terminus of p55.

Gag-Ma Function & Host-Virus Protein Interactions:[TOP]

Interactions highlighted in the image:

Potential interactions (not in the image):

  • Interacts with Env gp41 C-terminus .

Genomic Location & Protein Sequence: [TOP]

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
Position relative to Gag protein: 1 - 132

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 .
  • 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:

Primary and Secondary Database Entries: [TOP]


ViralZone: HIV-1, HIV replication cycle, HIV resource
PDB/MMDB: Search for HIV-1 & Matrix

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

InterPro: IPR000071
Pfam: PF00540
Prints: PR00234
SCOP: SSF47836 Retroviral matrix protein
BLOCKS: P04591
Prosite: P04591
ProtoNet: P04591
Database of Interacting Proteins: P04591
ModBase: P04591
HIV-1/Human Protein Interaction DB: HIV-1 Gag
HIV-1 Sequence Database Los Alamos HIV Sequence Database


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]
9 - Role of the HIV-1 Matrix Protein in Gag Intracellular Trafficking and Targeting to the Plasma Membrane for Virus Assembly.
Ghanam RH, Samal AB, Fernandez TF, Saad JS.
Front Microbiol. 17;3:55 (2012) [pubmed: 22363329]
10 - Structural basis for targeting HIV-1 Gag proteins to the plasma membrane for virus assembly.
Saad JS, Miller J, Tai J, Kim A, Ghanam RH, Summers MF.
Proc Natl Acad Sci U S A. 103(30):11364-9 (2006) [pubmed: 16840558]
11 - The role of matrix in HIV-1 envelope glycoprotein incorporation.
Tedbury PR, Freed EO.
Trends Microbiol. 22(7):372-8 (2014) [pubmed: 24933691]
12 - Two nuclear localization signals in the HIV-1 matrix protein regulate nuclear import of the HIV-1 pre-integration complex.
Haffar OK, Popov S, Dubrovsky L, Agostini I, Tang H, Pushkarsky T, Nadler SG, Bukrinsky M.
J Mol Biol. 299(2):359-68 (2000) [pubmed: 10860744]
13 - Molecular determinants that regulate plasma membrane association of HIV-1 Gag.
Chukkapalli V, Ono A.
J Mol Biol. 410(4):512-24 (2011) [pubmed: 21762797]
14 - Solution structure of calmodulin bound to the binding domain of the HIV-1 matrix protein.
Vlach J, Samal AB, Saad JS.
J Biol Chem. 289(12):8697-705 (2014) [pubmed: 24500712]
15 - Interaction of HIV-1 Gag with the clathrin-associated adaptor AP-2.
Batonick M, Favre M, Boge M, Spearman P, Höning S, Thali M.
Virology. 342(2):190-200 (2005) [pubmed: 16139856]
16 - AP-3 directs the intracellular trafficking of HIV-1 Gag and plays a key role in particle assembly.
Dong X, Li H, Derdowski A, Ding L, Burnett A, Chen X, Peters TR, Dermody TS, Woodruff E, Wang JJ, Spearman P.
Cell. 120(5):663-74 (2005) [pubmed: 15766529]
17 - Evidence in support of RNA-mediated inhibition of phosphatidylserine-dependent HIV-1 Gag membrane binding in cells.
Chukkapalli V, Inlora J, Todd GC, Ono A.
J Virol. 87(12):7155-9 (2013) [pubmed: 23552424]
18 - Solution X-ray scattering reveals a novel structure of calmodulin complexed with a binding domain peptide from the HIV-1 matrix protein p17.
Izumi Y, Watanabe H, Watanabe N, Aoyama A, Jinbo Y, Hayashi N.
Biochemistry 47(27):7158-66 (2008) [pubmed: 18553937]

Thanks to ViralZone at the Swiss Institute of Bioinformatics (SIB) for allowing the use of their images on
Page last updated by Megan Druce, Paula Sommer and Tulio de Oliveira (UKZN/Africa Centre) & Philippe Le Mercier, Chantal Hulo and Patrick Masson (SIB/ViralZone).