4NX4

Re-refinement of CAP-1 HIV-CA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2PXR - determined by Kelly, B.N.  

Literature

Protein structural ensembles are revealed by redefining X-ray electron density noise.

Lang, P.T.Holton, J.M.Fraser, J.S.Alber, T.

(2014) Proc.Natl.Acad.Sci.USA 111: 237-242

  • DOI: 10.1073/pnas.1302823110

  • PubMed Abstract: 
  • To increase the power of X-ray crystallography to determine not only the structures but also the motions of biomolecules, we developed methods to address two classic crystallographic problems: putting electron density maps on the absolute scale of e( ...

    To increase the power of X-ray crystallography to determine not only the structures but also the motions of biomolecules, we developed methods to address two classic crystallographic problems: putting electron density maps on the absolute scale of e(-)/Å(3) and calculating the noise at every point in the map. We find that noise varies with position and is often six to eight times lower than thresholds currently used in model building. Analyzing the rescaled electron density maps from 485 representative proteins revealed unmodeled conformations above the estimated noise for 45% of side chains and a previously hidden, low-occupancy inhibitor of HIV capsid protein. Comparing the electron density maps in the free and nucleotide-bound structures of three human protein kinases suggested that substrate binding perturbs distinct intrinsic allosteric networks that link the active site to surfaces that recognize regulatory proteins. These results illustrate general approaches to identify and analyze alternative conformations, low-occupancy small molecules, solvent distributions, communication pathways, and protein motions.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein
C
146Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
JPR
Query on JPR

Download SDF File 
Download CCD File 
C
1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)thio]ethyl}urea
C18 H24 Cl N3 O2 S
WEYNBWVKOYCCQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.145 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 42.187α = 90.00
b = 62.777β = 90.00
c = 106.286γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release