4NX4

Re-refinement of CAP-1 HIV-CA complex

Summary for 4NX4

• Entry DOI: 10.2210/pdb4nx4/pdb
• Related: 2JPR
• Descriptor: Gag-Pol polyprotein, CHLORIDE ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: capsid, viral protein
• Biological source: Human immunodeficiency virus type 1 (HIV-1)
• Cellular location: Matrix protein p17: Virion (Potential). Capsid protein p24: Virion (Potential). Nucleocapsid protein p7: Virion (Potential). Reverse transcriptase/ribonuclease H: Virion (Potential). Integrase: Virion (Potential): P12497
• Total number of polymer chains: 1
• Total formula weight: 16752.76

Authors

Lang, P.T.,Holton, J.M.,Fraser, J.S.,Alber, T. (deposition date: 2013-12-08, release date: 2014-02-26, Last modification date: 2024-02-28)

Primary citation

Lang, P.T.,Holton, J.M.,Fraser, J.S.,Alber, T.
Protein structural ensembles are revealed by redefining X-ray electron density noise.
Proc.Natl.Acad.Sci.USA, 111:237-242, 2014

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(-)/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.

PubMed: 24363322
DOI: 10.1073/pnas.1302823110

Experimental method

X-RAY DIFFRACTION (1.5 Å)