NC - P7, Nucleo-Capsid protein

HIV NC binds to the HIV packaging signal on viral RNA and is sufficient for incorporation of RNA into virions.

PDB-1A1T: HIV-1 (isolate NL4-3) Nucleo-Capsid (Chain A) and SL3 Stem-loop RNA (Chain B) - produced using SwissModel/SPDBV/POVray
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PDB: 1A1T (HIV-1 Nucleo-capsid)
SwissProt: P04591 (HIV-1 HXB2 GAG)
Chime Tutorial: not available
Los Alamos HIV structure DB: Nucleocapsid protein
EMBL: K03455 [EMBL/GenBank/DDBJ]
BioAfrica: Gag Protein Data Mining Tool


  • p7 (55 amino acids)

Cleavage site:


  • Virion
  • Cell cytoplasm


  • Encapsulates and protects viral dimeric unspliced (genomic) RNA (Ref. #7)
  • Incorporates viral RNA into virion
  • Specific recognition of HIV packaging signal of viral RNA (Ref. #4)

Additional Information:

  • the HIV packaging signal consists of 4 stem-loop structures near the 5'-end of viral RNA
  • the HIV packaging signal is sufficient to mediate the incorporation of heterologous RNA into virions (Ref. #5)
  • NC contains two zinc-finger motifs, which interact with the 4 stem-loop structures of the HIV packaging signal (Ref. #6)

Genomic Location: [TOP]

Reference Sequences:

HIV-1 (HXB2):

          10         20         30         40         50 
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[download in fasta format]

Length: 55 amino acids
Molecular Weight: 6425 Da
Theoretical pI: 10.08

Protein Domains/Folds/Motifs: [TOP]

InterPro signature for Retroviral NucleoCapsid protein Gag - IPR000721

Secondary Structure prediction:

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]

  • NC contains two zinc-finger motifs, which interact with the 4 stem-loop structures of the HIV packaging signal (Ref. #6)
  • the HIV packaging signal consists of 4 stem-loop structures near the 5'-end of viral RNA
  • NC binds to the psi site
  • NC binds to Reverse Transcriptase
  • NC binds to Vpr for Vpr incorporation into virions
  • NC binds to Actin during virus assembly

Primary and Secondary Database Entries: [TOP]


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

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

InterPro: IPR001878
Pfam: PF00607 / PF00098
Prints: none
ProDom: PD000129 (1 - 36) / PD506618 (3 - 37) / PD456461 (11 - 55) / PD594906 (14 - 51)
PD375076 (15 - 49) / PD107922 (15 -55) / PD019096 (15 -53) / PD406622 (37 -55)
SCOP: SSF57756 Retroviral zinc finger-like domains
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 - The human immunodeficiency virus type 1 packaging signal and major splice donor region
have a conserved stable secondary structure.
Harrison GP, Lever AM.
J Virol 66: 4144-4153 (1992) [pubmed: 1602537]
5 - Gene transfer into human lymphocytes by a defective human immunodeficiency virus type 1 vector.
Poznansky M, Lever A, Bergeron L.
J Virol 65: 532-536 (1991) [pubmed: 1985215]
6 - Interactions between HIV-1 nucleocapsid protein and viral DNA may have important functions
in the viral life cycle.
Lapadat-Tapolsky M, De Rocquigny H, Van Gent D.
Nucleic Acids Res 21: 831-839 (1993) [pubmed: 8383840]
7 - The chaperoning and assistance roles of the HIV-1 nucleocapsid protein in proviral DNA synthesis and  maintenance.
Bampi C, Jacquenet S, Lener D, Décimo D, Darlix JL.
Int J Biochem Cell Biol. 36(9):1668-86 (2004). [pubmed: 15183337]

Page last updated by Tulio de Oliveira.