ジャーナル: Cell / 年: 2005 タイトル: The cryo-EM structure of a translation initiation complex from Escherichia coli. 著者: Gregory S Allen / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank / 要旨: The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex ...The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex.
#241 - 2020年1月 20年の分子を振り返って (Twenty Years of Molecules) 類似性 (1)
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マップ
ファイル
ダウンロード / ファイル: emd_1248.map.gz / 形式: CCP4 / 大きさ: 8.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
This is a 3D volume map of an E. coli 70S translation initiation complex
ボクセルのサイズ
X=Y=Z: 2.82 Å
密度
表面レベル
1: 63.5 / ムービー #1: 30
最小 - 最大
-66.6267 - 212.468999999999994
平均 (標準偏差)
4.02043 (±25.465199999999999)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
-65
-65
-65
サイズ
130
130
130
Spacing
130
130
130
セル
A=B=C: 366.6 Å α=β=γ: 90 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.82
2.82
2.82
M x/y/z
130
130
130
origin x/y/z
0.000
0.000
0.000
length x/y/z
366.600
366.600
366.600
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-64
-64
-64
NX/NY/NZ
128
128
128
MAP C/R/S
1
2
3
start NC/NR/NS
-65
-65
-65
NC/NR/NS
130
130
130
D min/max/mean
-66.627
212.469
4.020
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添付データ
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試料の構成要素
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全体 : E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP
全体
名称: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP
要素
試料: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP
複合体: 30S
複合体: 50s
RNA: fmet-tRNA
RNA: mRNA
タンパク質・ペプチド: beta IF2-GDPNP
タンパク質・ペプチド: IF1
タンパク質・ペプチド: IF3
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超分子 #1000: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP
超分子
名称: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP タイプ: sample / ID: 1000 / 集合状態: One of each component binds to the 70S / Number unique components: 7
automated particle picking followed by manual verification
CTF補正
詳細: defocus groups
最終 再構成
想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 13.8 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: SPIDER 詳細: The falloff of Fourier amplitudes toward higher spatial frequencies was corrected using the x-ray solution scattering intensity distribution of 70S ribosomes from E. coli during each round of refinement. 使用した粒子像数: 20283
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原子モデル構築 1
ソフトウェア
名称: RSRef
詳細
Protocol: real-space refinement of rigid bodies. IF2 and IF1 were initially fit by hand in O then refined by RSRef
精密化
空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: correlation coefficient
得られたモデル
PDB-1zo1: IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiation complex
PDB-1zo3: The P-site and P/E-site tRNA structures fitted to P/I site codon.