PDBsum entry 1a43

Viral protein

PDB id: 1a43

Contents

Protein chain

72 a.a.

Waters ×28

PDB id:

1a43

Name:

Viral protein

Title:

Structure of the HIV-1 capsid protein dimerization domain at 2.6a resolution

Structure:

HIV-1 capsid. Chain: a. Fragment: c-terminal domain of HIV-1 capsid protein residues 146-231 (capsid numbering). Engineered: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.223 R-free: 0.281

Authors:

D.K.Worthylake,H.Wang,S.Yoo,W.I.Sundquist,C.P.Hill

Key ref:

D.K.Worthylake et al. (1999). Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution. Acta Crystallogr D Biol Crystallogr, 55, 85-92. PubMed id: 10089398 DOI: 10.1107/S0907444998007689

Date:

10-Feb-98 Release date: 09-Feb-99

Protein chain

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 72 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.1.-.-
• Enzyme class 5: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444998007689

Acta Crystallogr D Biol Crystallogr 55:85-92 (1999)

PubMed id: 10089398

Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution.

D.K.Worthylake, H.Wang, S.Yoo, W.I.Sundquist, C.P.Hill.

ABSTRACT

The human immunodeficiency virus type I (HIV-1) capsid protein is initially synthesized as the central domain of the Gag polyprotein, and is subsequently proteolytically processed into a discrete 231-amino-acid protein that forms the distinctive conical core of the mature virus. The crystal structures of two proteins that span the C-terminal domain of the capsid are reported here: one encompassing residues 146-231 (CA146-231) and the other extending to include the 14-residue p2 domain of Gag (CA146-p2). The isomorphous CA146-231 and CA146-p2 structures were determined by molecular replacement and have been refined at 2.6 A resolution to R factors of 22.3 and 20.7% (Rfree = 28.1 and 27.5%), respectively. The ordered domains comprise residues 148-219 for CA146-231 and 148-218 for CA146-p2, and their refined structures are essentially identical. The proteins are composed of a 310 helix followed by an extended strand and four alpha-helices. A crystallographic twofold generates a dimer that is stabilized by parallel packing of an alpha-helix 2 across the dimer interface and by packing of the 310 helix into a groove created by alpha-helices 2 and 3 of the partner molecule. CA146-231 and CA146-p2 dimerize with the full affinity of the intact capsid protein, and their structures therefore reveal the essential dimer interface of the HIV-1 capsid.

Selected figure(s)

Figure 5.
Figure 5 View of the CA[146-231]/CA[146-p2] dimer-interface residues. Residues that appear to lose more than 5 Å^2 of solvent-accessible surface area upon dimer formation are shown explicitly. Orientation and color code are the same as for Fig. 3-.

Figure 6.
Figure 6 Model of the full-length capsid protein. N-terminal domains (residues 1-145) are colored magenta and C-terminal domain dimer (residues 148-219) are colored blue. The disordered residues Ser146 and Pro147 which link the N- and C-terminal domains are colored gray. The C-terminal dimer is oriented with the twofold axis vertical. Atomic models of the full-length capsid protein were built using the crystal structures of the N- and C-terminal domains of capsid (Gamble et al., 1996[Gamble, T. R., Vajdos, F. F., Yoo, S., Worthylake, D. K., Houseweart, M., Sundquist, W. I. & Hill, C. P. (1996). Cell, 87, 1285-1294.]). The last ordered residue of the N-terminal domain (Tyr145) was covalently connected to the first ordered residue of the C-terminal domain (Thr148) with a dipeptide linker (Ser146-Pro147). Plausible conformations for the Ser146-Pro147 linker allowed models to be built that exhibited a wide ( 90°) range of relative rotations between the two domains.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 85-92) copyright 1999.

Figures were selected by an automated process.