Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-626529 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom
要素
(Envelope glycoprotein ...) x 2
35O22 FAB HEAVY CHAIN
35O22 FAB LIGHT CHAIN
PGT122 FAB HEAVY CHAIN
PGT122 FAB LIGHT CHAIN
キーワード
VIRAL PROTEIN/Immune System / HIV-1 entry / small molecule / inhibitor / VIRAL PROTEIN-Immune System complex
機能・相同性
機能・相同性情報
positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane 類似検索 - 分子機能
B: Envelope glycoprotein gp160 D: 35O22 FAB HEAVY CHAIN E: 35O22 FAB LIGHT CHAIN G: Envelope glycoprotein gp160 H: PGT122 FAB HEAVY CHAIN L: PGT122 FAB LIGHT CHAIN ヘテロ分子
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 1 Å / 相対比: 1
反射
解像度: 3.02→50 Å / Num. obs: 43880 / % possible obs: 85.6 % / 冗長度: 2.6 % / Net I/σ(I): 2.2
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
(1.11.1_2575: ???)
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
PHASER
位相決定
精密化
解像度: 3.031→41.349 Å / SU ML: 0.58 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 40.62 / 立体化学のターゲット値: ML 詳細: AUTHORS STATE THAT THE OVERALL RESOLUTION WAS DETERMINED AS FOLLOWS: IT IS THE HIGHEST RESOLUTION FOR WHICH THE COMPLETENESS WAS GREATER THAN 50% AND THE I/SIGMAI WAS GREATER THAN 2.0. ...詳細: AUTHORS STATE THAT THE OVERALL RESOLUTION WAS DETERMINED AS FOLLOWS: IT IS THE HIGHEST RESOLUTION FOR WHICH THE COMPLETENESS WAS GREATER THAN 50% AND THE I/SIGMAI WAS GREATER THAN 2.0. CRYSTAL DIFFRACTION DATA WERE THEN ASSESSED FOR ANISOTROPY THROUGH USE OF THE DIFFRACTION ANISOTROPY SERVER (HTTP://SERVICES.MBI.UCLA.EDU/ANISOSCALE/), WHICH INDICATES THE RESOLUTION AT WHICH F/SIGMA DROPS BELOW 3.0 ALONG A, B, AND C AXES; THESE WERE 3.8 A, 3.8 A, 3.0 A. BECAUSE WE SOUGHT TO USE AS MUCH OF THE DATA AS POSSIBLE FOR REFINEMENT, WE USED THE OVERALL RESOLUTION DESCRIBED ABOVE TO DEFINE THE RESOLUTION OF THE A AND B AXES, WITH THE RESOLUTION LIMIT FOR THE C AXIS DEFINED BY THE DIFFRACTION ANISOTROPY SERVER.
Rfactor
反射数
%反射
Rfree
0.3254
1584
5.01 %
Rwork
0.2723
-
-
obs
0.2749
31627
54.07 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL