ジャーナル: Nucleic Acids Res / 年: 2015 タイトル: Structural basis for the interaction of protein S1 with the Escherichia coli ribosome. 著者: Konstantin Byrgazov / Irina Grishkovskaya / Stefan Arenz / Nicolas Coudevylle / Hannes Temmel / Daniel N Wilson / Kristina Djinovic-Carugo / Isabella Moll / 要旨: In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to ...In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to its functional importance, S1 is still lacking from the high-resolution structures available for Escherichia coli and Thermus thermophilus ribosomes and thus the molecular mechanism governing the S1-ribosome interaction has still remained elusive. Here, we present the structure of the N-terminal S1 domain D1 when bound to the ribosome at atomic resolution by using a combination of NMR, X-ray crystallography and cryo-electron microscopy. Together with biochemical assays, the structure reveals that S1 is anchored to the ribosome primarily via a stabilizing π-stacking interaction within the short but conserved N-terminal segment that is flexibly connected to domain D1. This interaction is further stabilized by salt bridges involving the zinc binding pocket of protein S2. Overall, this work provides one hitherto enigmatic piece in the 'ribosome puzzle', namely the detailed molecular insight into the topology of the S1-ribosome interface. Moreover, our data suggest novel mechanisms that have the potential to modulate protein synthesis in response to environmental cues by changing the affinity of S1 for the ribosome.
ダウンロード / ファイル: emd_6211.map.gz / 形式: CCP4 / 大きさ: 185.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
ボクセルのサイズ
X=Y=Z: 1.0489 Å
密度
表面レベル
登録者による: 0.0006 / ムービー #1: 0.0006
最小 - 最大
-0.00085958 - 0.00166435
平均 (標準偏差)
0.00001144 (±0.00015951)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
368
368
368
Spacing
368
368
368
セル
A=B=C: 385.9952 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.0488994565217
1.0488994565217
1.0488994565217
M x/y/z
368
368
368
origin x/y/z
0.000
0.000
0.000
length x/y/z
385.995
385.995
385.995
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-72
-72
-72
NX/NY/NZ
145
145
145
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
368
368
368
D min/max/mean
-0.001
0.002
0.000
-
添付データ
-
試料の構成要素
-
全体 : Reconstruction of ErmCL-stalled E. coli ribosome containing densi...
全体
名称: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
要素
試料: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
複合体: ErmCL-stalled ribosome
-
超分子 #1000: Reconstruction of ErmCL-stalled E. coli ribosome containing densi...
超分子
名称: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1 タイプ: sample / ID: 1000 / Number unique components: 1