[日本語] English
文献
- EMDB/PDB/SASBDBから引用されている文献のデータベース -

+
検索条件

キーワード
構造解析手法
著者・登録者
ジャーナル
IF

-
Structure paper

タイトルAssembly landscape for the bacterial large ribosomal subunit.
ジャーナル・号・ページNat Commun, Vol. 14, Issue 1, Page 5220, Year 2023
掲載日2023年8月26日
著者Kai Sheng / Ning Li / Jessica N Rabuck-Gibbons / Xiyu Dong / Dmitry Lyumkis / James R Williamson /
PubMed 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.
リンクNat Commun / PubMed:37633970 / PubMed Central
手法EM (単粒子)
解像度5.41 - 9.27 Å
構造データ

EMDB-40309: E. coli 50S assembly intermediate from bL17-depletion strain, class: rl17-B-b1
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40311: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b2
手法: EM (単粒子) / 解像度: 6.0 Å

EMDB-40312: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40313: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40314: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b1
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40315: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b2
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40316: E. coli 50S intermediate, srmB deletion strain, class: srmb-B-a1
手法: EM (単粒子) / 解像度: 9.27 Å

EMDB-40317: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40318: E. coli 50S intermediate, srmB deletion strain, class: srmb-B-a2
手法: EM (単粒子) / 解像度: 8.29 Å

EMDB-40319: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b4
手法: EM (単粒子) / 解像度: 5.54 Å

EMDB-40320: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a1
手法: EM (単粒子) / 解像度: 7.75 Å

EMDB-40321: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b5
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40322: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a2
手法: EM (単粒子) / 解像度: 8.08 Å

EMDB-40323: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b6
手法: EM (単粒子) / 解像度: 6.81 Å

EMDB-40324: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a3
手法: EM (単粒子) / 解像度: 6.81 Å

EMDB-40325: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a4
手法: EM (単粒子) / 解像度: 8.46 Å

EMDB-40327: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-a1
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40328: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a5
手法: EM (単粒子) / 解像度: 7.89 Å

EMDB-40329: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-a2
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40330: E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a1
手法: EM (単粒子) / 解像度: 7.56 Å

EMDB-40331: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-a3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40332: E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a2
手法: EM (単粒子) / 解像度: 7.77 Å

EMDB-40333: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b1
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40511: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b4
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40512: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b2
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40513: E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a3
手法: EM (単粒子) / 解像度: 6.99 Å

EMDB-40514: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40515: E. coli 50S intermediate, srmB deletion strain, class: srmb-G1
手法: EM (単粒子) / 解像度: 6.84 Å

EMDB-40516: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b4
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40517: E. coli 50S intermediate, srmB deletion strain, class: dead-B-a1
手法: EM (単粒子) / 解像度: 5.91 Å

EMDB-40518: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a1
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40519: E. coli 50S intermediate, srmB deletion strain, class: dead-B-a2
手法: EM (単粒子) / 解像度: 5.41 Å

EMDB-40520: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a2
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40521: E. coli 50S intermediate, srmB deletion strain, class: dead-B-a3
手法: EM (単粒子) / 解像度: 5.62 Å

EMDB-40523: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40524: E. coli 50S intermediate, deaD deletion strain, class: dead-B-a4
手法: EM (単粒子) / 解像度: 5.41 Å

EMDB-40525: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a4
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40526: E. coli 50S intermediate, deaD deletion strain, class: dead-B-a5
手法: EM (単粒子) / 解像度: 6.24 Å

EMDB-40527: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a5
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40528: E. coli 50S intermediate, deaD deletion strain, class: dead-B-a6
手法: EM (単粒子) / 解像度: 5.99 Å

EMDB-40529: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b1
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40530: E. coli 50S intermediate, deaD deletion strain, class: dead-B-b1
手法: EM (単粒子) / 解像度: 6.43 Å

EMDB-40531: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b10
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40532: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a1
手法: EM (単粒子) / 解像度: 6.14 Å

EMDB-40533: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b2
手法: EM (単粒子) / 解像度: 5.68 Å

EMDB-40534: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a2
手法: EM (単粒子) / 解像度: 5.96 Å

EMDB-40535: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b3
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40536: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a3
手法: EM (単粒子) / 解像度: 6.16 Å

EMDB-40537: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b4
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40538: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a4
手法: EM (単粒子) / 解像度: 5.41 Å

EMDB-40539: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b5
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40540: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a5
手法: EM (単粒子) / 解像度: 6.27 Å

EMDB-40541: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b6
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40542: E. coli 50S intermediate, deaD deletion strain, class: dead-C-b1
手法: EM (単粒子) / 解像度: 5.41 Å

EMDB-40543: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b7
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40544: E. coli 50S intermediate, deaD deletion strain, class: dead-C-b2
手法: EM (単粒子) / 解像度: 5.41 Å

EMDB-40545: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b8
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40546: E. coli 50S intermediate, deaD deletion strain, class: dead-E-a1
手法: EM (単粒子) / 解像度: 5.43 Å

EMDB-40547: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b9
手法: EM (単粒子) / 解像度: 5.45 Å

EMDB-40548: E. coli 50S intermediate, deaD deletion strain, class: dead-G1
手法: EM (単粒子) / 解像度: 6.74 Å

EMDB-40549: E. coli 50S intermediate, deaD deletion strain, class: dead-preB2
手法: EM (単粒子) / 解像度: 7.36 Å

EMDB-40550: E. coli 50S intermediate, deaD deletion strain, class: dead-G2
手法: EM (単粒子) / 解像度: 5.89 Å

EMDB-40551: E. coli 50S intermediate, deaD deletion strain, class: dead-preB1
手法: EM (単粒子) / 解像度: 6.39 Å

EMDB-40552: E. coli 50S intermediate, deaD deletion strain, class: dead-G3
手法: EM (単粒子) / 解像度: 5.41 Å

EMDB-40555: E. coli 50S intermediate, deaD deletion strain, class: dead-G4
手法: EM (単粒子) / 解像度: 5.74 Å

由来
  • Escherichia coli K-12 (大腸菌)

+
万見文献について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見文献

EMDB/PDB/SASBDBから引用されている文献のデータベース

  • EMDB/PDB/SASBDBのエントリから引用されている文献のデータベースです
  • Pubmedのデータを利用しています

関連情報:EMDB / PDB / SASBDB / 万見 (Yorodumi) / EMN文献 / 新しいEM Navigatorと万見の変更点

他の情報も見る