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 and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 8.54 kDa 
• Atom Count: 580 
• Residue Count: 73 
• Unique protein chains: 1

2ONT

A swapped dimer of the HIV-1 capsid C-terminal domain

• DOI: 10.2210/pdb2ONT/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-24 Released: 2007-02-20 
• Deposition Author(s): Ivanov, D., Tsodikov, O.V., Kasanov, J., Ellenberger, T., Wagner, G., Collins, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.243 
• R-Value Observed: 0.246 

Literature

Domain-swapped dimerization of the HIV-1 capsid C-terminal domain

Ivanov, D., Tsodikov, O.V., Kasanov, J., Ellenberger, T., Wagner, G., Collins, T.

(2007) Proc Natl Acad Sci U S A 104: 4353-4358

• PubMed: 17360528 
• DOI: 10.1073/pnas.0609477104
• Primary Citation of Related Structures:  
  2ONT


• PubMed Abstract: 
  

Assembly of the HIV and other retroviruses is primarily driven by the oligomerization of the Gag polyprotein, the major viral structural protein capable of forming virus-like particles even in the absence of all other virally encoded components. Several critical determinants of Gag oligomerization are located in the C-terminal domain of the capsid protein (CA-CTD), which encompasses the most conserved segment in the highly variable Gag protein called the major homology region (MHR). The CA-CTD is thought to function as a dimerization module, although the existing model of CA-CTD dimerization does not readily explain why the conserved residues of the MHR are essential for retroviral assembly. Here we describe an x-ray structure of a distinct domain-swapped variant of the HIV-1 CA-CTD dimer stabilized by a single amino acid deletion. In the domain-swapped structure, the MHR-containing segment forms a major part of the dimerization interface, providing a structural mechanism for the enigmatic function of the MHR in HIV assembly. Our observations suggest that swapping of the MHR segments of adjacent Gag molecules may be a critical intermediate in retroviral assembly.

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Organizational Affiliation: 

Department of Pathology, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A	76	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 0  Gene Names: gag-pol
Find proteins for Q9IVQ4 (Human immunodeficiency virus 1) Explore Q9IVQ4  Go to UniProtKB:  Q9IVQ4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.243 
• R-Value Observed: 0.246 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.129	α = 90
b = 40.129	β = 90
c = 105.322	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-24 
• Released Date: 2007-02-20 
Deposition Author(s): Ivanov, D., Tsodikov, O.V., Kasanov, J., Ellenberger, T., Wagner, G., Collins, T.

Revision History 

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance