E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b3
マップデータ
rl17-C-b3 Class Particle stack from (doi: 10.1016/j.cell.2016.11.020.) was reanalyzed by CryoSPARC ab-initio subclassification. Aligned to 50S reference and resample to same gird.
試料
複合体: E. coli 50S assembly intermediate from bL17-depletion strain
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM-136412
米国
引用
ジャーナル: Nat Commun / 年: 2023 タイトル: Assembly landscape for the bacterial large ribosomal subunit. 著者: Kai Sheng / Ning Li / Jessica N Rabuck-Gibbons / Xiyu Dong / Dmitry Lyumkis / James R Williamson / 要旨: Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic ...Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions.
ダウンロード / ファイル: emd_40317.map.gz / 形式: CCP4 / 大きさ: 15.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
rl17-C-b3 Class Particle stack from (doi: 10.1016/j.cell.2016.11.020.) was reanalyzed by CryoSPARC ab-initio subclassification. Aligned to 50S reference and resample to same gird.
ボクセルのサイズ
X=Y=Z: 2.62 Å
密度
表面レベル
登録者による: 1.0
最小 - 最大
-1.6998471 - 4.962919
平均 (標準偏差)
-0.00506049 (±0.25543052)
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
160
160
160
Spacing
160
160
160
セル
A=B=C: 419.19998 Å α=β=γ: 90.0 °
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添付データ
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ハーフマップ: rl17-C-b3 Class Particle stack from (doi: 10.1016/j.cell.2016.11.020.) was...
全体 : E. coli 50S assembly intermediate from bL17-depletion strain
全体
名称: E. coli 50S assembly intermediate from bL17-depletion strain
要素
複合体: E. coli 50S assembly intermediate from bL17-depletion strain
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超分子 #1: E. coli 50S assembly intermediate from bL17-depletion strain
超分子
名称: E. coli 50S assembly intermediate from bL17-depletion strain タイプ: complex / ID: 1 / 親要素: 0
由来(天然)
生物種: Escherichia coli K-12 (大腸菌)
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実験情報
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構造解析
手法
クライオ電子顕微鏡法
解析
単粒子再構成法
試料の集合状態
particle
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試料調製
緩衝液
pH: 7.5 構成要素:
濃度
名称
式
20.0 mM
Tris-HCl
100.0 mM
ammonium chloride
NH4Cl
10.0 mM
magnesium chloride
MgCl2
0.5 mM
EDTA
6.0 mM
beta-mercaptoethanol
凍結
凍結剤: ETHANE / チャンバー内湿度: 100 %
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電子顕微鏡法
顕微鏡
FEI TITAN KRIOS
撮影
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 33.0 e/Å2 詳細: data were collected with tilts ranging from 0 to 60 degree at 10-degree increments