4NX4

Re-refinement of CAP-1 HIV-CA complex

4NX4 の概要

• エントリーDOI: 10.2210/pdb4nx4/pdb
• 関連するPDBエントリー: 2JPR
• 分子名称: Gag-Pol polyprotein, CHLORIDE ION, ZINC ION, ... (5 entities in total)
• 機能のキーワード: capsid, viral protein
• 由来する生物種: Human immunodeficiency virus type 1 (HIV-1)
• 細胞内の位置: 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
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16752.76

構造登録者

Lang, P.T.,Holton, J.M.,Fraser, J.S.,Alber, T. (登録日: 2013-12-08, 公開日: 2014-02-26, 最終更新日: 2024-02-28)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.5 Å)