2PWO

Crystal Structure of HIV-1 CA146 A92E Psuedo Cell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Antiviral Assembly Inhibitor CAP-1 Complex with the HIV-1 CA Protein.

Kelly, B.N.Kyere, S.Kinde, I.Tang, C.Howard, B.R.Robinson, H.Sundquist, W.I.Summers, M.F.Hill, C.P.

(2007) J Mol Biol 373: 355-366

  • DOI: 10.1016/j.jmb.2007.07.070
  • Primary Citation of Related Structures:  
    2JPR, 2PWO, 2PWM, 2PXR

  • PubMed Abstract: 
  • The CA domain of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein plays critical roles in both the early and late phases of viral replication and is therefore an attractive antiviral target. Compounds with antiviral activity were recently ...

    The CA domain of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein plays critical roles in both the early and late phases of viral replication and is therefore an attractive antiviral target. Compounds with antiviral activity were recently identified that bind to the N-terminal domain of CA (CA N) and inhibit capsid assembly during viral maturation. We have determined the structure of the complex between CA N and the antiviral assembly inhibitor N-(3-chloro-4-methylphenyl)-N'-{2-[({5-[(dimethylamino)-methyl]-2-furyl}-methyl)-sulfanyl]ethyl}-urea) (CAP-1) using a combination of NMR spectroscopy and X-ray crystallography. The protein undergoes a remarkable conformational change upon CAP-1 binding, in which Phe32 is displaced from its buried position in the protein core to open a deep hydrophobic cavity that serves as the ligand binding site. The aromatic ring of CAP-1 inserts into the cavity, with the urea NH groups forming hydrogen bonds with the backbone oxygen of Val59 and the dimethylamonium group interacting with the side-chains of Glu28 and Glu29. Elements that could be exploited to improve binding affinity are apparent in the structure. The displacement of Phe32 by CAP-1 appears to be facilitated by a strained main-chain conformation, which suggests a potential role for a Phe32 conformational switch during normal capsid assembly.


    Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gag-Pol polyprotein (Pr160Gag-Pol) ABCD146Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag-polgag
Find proteins for A9PKC6 (Human immunodeficiency virus 1)
Explore A9PKC6 
Go to UniProtKB:  A9PKC6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.225α = 83.01
b = 48.208β = 71.28
c = 58.928γ = 87.43
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-05-11 
  • Released Date: 2007-09-25 
  • Deposition Author(s): Kelly, B.N.

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description