4NX4 image
Deposition Date 2013-12-08
Release Date 2014-02-26
Last Version Date 2024-02-28
Entry Detail
PDB ID:
4NX4
Keywords:
Title:
Re-refinement of CAP-1 HIV-CA complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.50 Å
R-Value Free:
0.19
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Gag-Pol polyprotein
Gene (Uniprot):gag-pol
Chain IDs:A (auth: C)
Chain Length:146
Number of Molecules:1
Biological Source:Human immunodeficiency virus type 1
Primary Citation
Protein structural ensembles are revealed by redefining X-ray electron density noise.
Proc.Natl.Acad.Sci.USA 111 237 242 (2014)
PMID: 24363322 DOI: 10.1073/pnas.1302823110

Abstact

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.

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