E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a1
マップデータ
srmb-E-a1 class Particle stack from (doi: 10.1016/j.jmb.2019.12.013. Epub 2019 Dec 23.) was reanalyzed by CryoSPARC ab-initio subclassification. Aligned to 50S ref and resample to same grid.
試料
複合体: E. coli 50S intermediate, srmB deletion 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_40330.map.gz / 形式: CCP4 / 大きさ: 15.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
srmb-E-a1 class Particle stack from (doi: 10.1016/j.jmb.2019.12.013. Epub 2019 Dec 23.) was reanalyzed by CryoSPARC ab-initio subclassification. Aligned to 50S ref and resample to same grid.
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
-0.78456664 - 2.6759021
平均 (標準偏差)
0.00769939 (±0.17903073)
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: srmb-E-a1 class Particle stack from (doi: 10.1016/j.jmb.2019.12.013. Epub...
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: 45.0 e/Å2 詳細: data were collected with tilts ranging from 0 to 60 degree at 10-degree increments