2BUO | pdb_00002buo

HIV-1 capsid C-terminal domain in complex with an inhibitor of particle assembly

• PDB DOI: https://doi.org/10.2210/pdb2BUO/pdb

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


• Deposited: 2005-06-17 Released: 2005-07-21 
• Deposition Author(s): Ternois, F., Sticht, J., Duquerroy, S., Krausslich, H.-G., Rey, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.234 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

The HIV-1 Capsid Protein C-Terminal Domain in Complex with a Virus Assembly Inhibitor

Ternois, F., Sticht, J., Duquerroy, S., Krausslich, H.-G., Rey, F.A.

(2005) Nat Struct Mol Biol 12: 678

• PubMed: 16041386 
• DOI: https://doi.org/10.1038/nsmb967
• Primary Citation Related Structures: 
  2BUO


• PubMed Abstract: 
  

  Immature HIV particles bud from infected cells after assembly at the cytoplasmic side of cellular membranes. This assembly is driven by interactions between Gag polyproteins. Mature particles, each containing a characteristic conical core, are later generated by proteolytic maturation of Gag in the virion. The C-terminal domain of the HIV-1 capsid protein (C-CA) has been shown to contain oligomerization determinants essential for particle assembly. Here we report the 1.7-A-resolution crystal structure of C-CA in complex with a peptide capable of inhibiting immature- and mature-like particle assembly in vitro. The peptide inserts as an amphipathic alpha-helix into a conserved hydrophobic groove of C-CA, resulting in formation of a compact five-helix bundle with altered dimeric interactions. This structure thus reveals the details of an allosteric site in the HIV capsid protein that can be targeted for antiviral therapy.

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Organizational Affiliation: 
• Laboratoire de Virologie Moléculaire & Structurale, UMR 2472/1157 CNRS-INRA and IFR 115, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 11.04 kDa 
• Atom Count: 894 
• Modeled Residue Count: 97 
• Deposited Residue Count: 98 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 CAPSID PROTEIN	A	86	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P03347 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03347  Go to UniProtKB:  P03347

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR OF CAPSID ASSEMBLY	B [auth T]	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.234 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.541	α = 90
b = 42.541	β = 90
c = 90.903	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-21 
Deposition Author(s): Ternois, F., Sticht, J., Duquerroy, S., Krausslich, H.-G., Rey, F.A.

Revision History  

• Version 1.0: 2005-07-21
  Type: Initial release
  
• Version 1.1: 2017-02-15
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description