ジャーナル: Proc Natl Acad Sci U S A / 年: 2015 タイトル: Structure of BipA in GTP form bound to the ratcheted ribosome. 著者: Veerendra Kumar / Yun Chen / Rya Ero / Tofayel Ahmed / Jackie Tan / Zhe Li / Andrew See Weng Wong / Shashi Bhushan / Yong-Gui Gao / 要旨: BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly ...BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.
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: 4→47.9 Å / Num. obs: 10792 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / 冗長度: 18.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 14
反射 シェル
解像度: 4→4.24 Å / 冗長度: 18 % / Mean I/σ(I) obs: 0.82 / % possible all: 99.2
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0107
精密化
XDS
データ削減
XDS
データスケーリング
MOLREP
位相決定
精密化
構造決定の手法: 分子置換 開始モデル: BIPA 解像度: 4→47.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 127.694 / SU ML: 1.354 / 交差検証法: THROUGHOUT / ESU R Free: 0.872 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
Rfactor
反射数
%反射
Selection details
Rfree
0.321
809
7.5 %
RANDOM
Rwork
0.25392
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-
-
obs
0.259
9974
99.59 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK