Function of HIV Capsid

• HIV Capsid is a structural protein encoded by the gag gene which provides the basic infrastructure of viral particles [1].

• The hexamer and pentamer structure of Capsid constitutes the conical fullerene core of mature HIV particles [2].

• The interaction between Capsid and host proteins allows for the packaging of host proteins (e.g. cyclophilin A) into HIV particles. Capsid also binds with the host restriction factor TRIM5α to prevent viral uncoating at the early stage [3].

Reference

1. Bell, N. M. & Lever, A. M. HIV Gag polyprotein: processing and early viral particle assembly. Trends in microbiology 21, 136-144, (2013).(Download Article)

2. Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497, 643-646, (2013).(Download Article)

3. Luban, J. TRIM5 and the Regulation of HIV-1 Infectivity. Molecular biology international 2012, 426840, (2012). (Download Article)

Sequence

(1) Reference sequence for HIV-1 Capsid

• Strain: HIV-1 subtype B HXB2 (ID: K03455)

• Fasta format: Download

• Reference sequence:

  1       10         20         30         40         50
  |        |          |          |          |          | 
  PIVQNIQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAGP IAPGQMREPR 
  101    110        120        130        140        150
  |        |          |          |          |          | 
  GSDIAGTTST LQEQIGWMTN NPPIPVGEIY KRWIILGLNK IVRMYSPTSI 
  151    160        170        180        190        200
  |        |          |          |          |          | 
  LDIRQGPKEP FRDYVDRFYK TLRAEQASQE VKNWMTETLL VQNANPDCKT 
  201    210        220        230
  |        |          |          | 
  ILKALGPAAT LEEMMTACQG VGGPGHKARV L 

(2) Reference sequence for HIV-2 and SIV Capsid

• Strain: SIV Mac239 (ID: M33262)

• Fasta format: Download

• Reference sequence:

  1       10         20         30         40         50
  |        |          |          |          |          | 
  PVQQIGGNYV HLPLSPRTLN AWVKLIEEKK FGAEVVPGFQ ALSEGCTPYD 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  INQMLNCVGD HQAAMQIIRD IINEEAADWD LQHPQPAPQQ GQLREPSGSD 
  101    110        120        130        140        150
  |        |          |          |          |          | 
  IAGTTSSVDE QIQWMYRQQN PIPVGNIYRR WIQLGLQKCV RMYNPTNILD 
  151    160        170        180        190        200
  |        |          |          |          |          | 
  VKQGPKEPFQ SYVDRFYKSL RAEQTDAAVK NWMTQTLLIQ NANPDCKLVL 
  201    210        220
  |        |          | 
  KGLGVNPTLE EMLTACQGVG GPGQKARLM 

(3) Coloring scheme for above amino acids

1. Amino acids with hydrophobic side chains (normally buried inside the protein core):

   • A - Ala - Alanine

   • I - Ile - Isoleucine

   • L - Leu - Leucine

   • M - Met - Methionine

   • V - Val - Valine

2. Amino acids with polar uncharged side chains (may participate in hydrogen bonds):

   • N - Asn - Asparagine

   • Q - Gln - Glutamine

   • S - Ser - Serine

   • T - Thr - Threonine

3. Amino acids with positive charged side chains:

   • H - His - Histidine

   • K - Lys - Lysine

   • R - Arg - Arginine

4. Amino acids with negative charged side chains:

   • D - Asp - Aspartic acid

   • E - Glu - Glutamic acid

5. Amino acids with aromatic side chains:

   • F - Phe - Phenylalanine

   • Y - Tyr - Tyrosine

   • W - Trp - Tryptophan

6. Cysteine: C - Cys - Cysteine

7. Glycine: G - Gly - Glycine

8. Proline: P - Pro - Proline

Amino acid variations at HIV-1 Capsid

Here, we visualize the prevalence of amino acid variations at the HIV-1 Capsid from HIV-1 subtype B.

Protocal of our sequence collection

• For HIV-1 subtype B, one sequence per patient was extracted from HIV Los Alamos database (www.hiv.lanl.gov/).

• We removed misclassified sequences or sequences with hypermutations, stop codons, ambiguous nucleotides, which were described in our article [1].

• We removed sequences conferred partial or full resistance to any of the protease inhibitors, RT inhibitors and integrase inhibitors using HIVdb V6.0 .

Visualization

Our sequence dataset of HIV-1 subtype B Capsid included 4725 sequences. In the following picture, HXB2 indices of individual proteins are shown on top of the colored bars. A consensus amino acid at each position is shown beneath the colored bar. Natural variations are shown below the consensus amino acids; proportions (%) are colored red if they were more than 5%; blue otherwise.

HIV-1 protein interaction patterns.

Please cite our article:

1. Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne-Mieke Vandamme, Kristof Theys. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology 12, 18, doi:10.1186/s12977-015-0148-6 (2015). [PDF] [PubMed Link]

Structure

(1) Secondary structure of HIV-1 Capsid

Here, we visualize the secondary structure of HIV-1 Capsid using PDBSum (PDB code: 3H4E)

(2) Tertiary structure of HIV-1 Capsid

Here, we provide a structure movie of Capsid using PyMOL V1.7 (PDB code: 3H4E). Alpha-helix and beta-strand secondary structures are demonstrated by red .

Localization

(1) Coding region of Capsid at the HIV genome

(2) Localization of Capsid during the HIV-1 life cycle

Here, we visualize the localization of Capsid during the viral life cycle. Red stars indicate the appearance of HIV-1 Capsid.

Anti-HIV inhibitor

(1) Drug binding pocket of HIV-1 Capsid

Here, we visualize the drug binding pocket of HIV-1 Capsid

(2) List of known inhibitors targeting HIV-1 Capsid

Here, we summarize the published anti-HIV inhibitors which bind to HIV-1 Capsid.

Protein-protein interactions