Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.66 kDa 
• Atom Count: 600 
• Residue Count: 72 
• Unique protein chains: 1

1A43

STRUCTURE OF THE HIV-1 CAPSID PROTEIN DIMERIZATION DOMAIN AT 2.6A RESOLUTION

• DOI: 10.2210/pdb1A43/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-02-10 Released: 1999-02-09 
• Deposition Author(s): Worthylake, D.K., Wang, H., Yoo, S., Sundquist, W.I., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

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

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

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

• PubMed: 10089398 
• DOI: 10.1107/S0907444998007689
• Primary Citation of Related Structures:  
  1BAJ, 1A43


• PubMed 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.

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Organizational Affiliation: 

Biochemistry Department, University of Utah Medical School, 50 North Medical Drive, Salt Lake City, Utah 84132, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 CAPSID	A	87	Human immunodeficiency virus 1	Mutation(s): 0  EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.41	α = 90
b = 60.41	β = 90
c = 60.43	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-10 
• Released Date: 1999-02-09 
Deposition Author(s): Worthylake, D.K., Wang, H., Yoo, S., Sundquist, W.I., Hill, C.P.

Revision History 

• Version 1.0: 1999-02-09
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance