+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6h58 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome | |||||||||
要素 |
| |||||||||
キーワード | RIBOSOME / 100S / cryo-EM / E-site tRNA / hibernation / HPF / RMF / S1 | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / single-stranded RNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli BW25113 (大腸菌) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.9 Å | |||||||||
データ登録者 | Beckert, B. / Turk, M. / Czech, A. / Berninghausen, O. / Beckmann, R. / Ignatova, Z. / Plitzko, J. / Wilson, D.N. | |||||||||
資金援助 | ドイツ, 2件
| |||||||||
引用 | ジャーナル: Nat Microbiol / 年: 2018 タイトル: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. 著者: Bertrand Beckert / Martin Turk / Andreas Czech / Otto Berninghausen / Roland Beckmann / Zoya Ignatova / Jürgen M Plitzko / Daniel N Wilson / 要旨: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S ...To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6h58.cif.gz | 6.4 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6h58.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6h58.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6h58_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6h58_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 6h58_validation.xml.gz | 348.4 KB | 表示 | |
CIF形式データ | 6h58_validation.cif.gz | 679.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h58 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h58 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
+50S ribosomal protein ... , 29種, 58分子 000111222333444666CCCDDDEEEFFFGGGHHHJJJKKKLLL...
-RNA鎖 , 4種, 8分子 AAABBBaaawww
#7: RNA鎖 | 分子量: 941305.250 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli BW25113 (大腸菌) / 参照: GenBank: 1036415628 #8: RNA鎖 | 分子量: 38813.133 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli BW25113 (大腸菌) / 参照: GenBank: 1393501787 #32: RNA鎖 | 分子量: 498725.406 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli BW25113 (大腸菌) / 参照: GenBank: 1359176725 #56: RNA鎖 | 分子量: 24771.770 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli BW25113 (大腸菌) / 参照: GenBank: 1063812051 |
---|
+30S ribosomal protein ... , 21種, 42分子 bbbcccdddeeefffggghhhiiijjjkkklllmmmnnnoooppp...
-タンパク質 , 2種, 4分子 vvvxxx
#53: タンパク質 | 分子量: 6520.523 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli BW25113 (大腸菌) / 参照: UniProt: P0AFW2 #54: タンパク質 | 分子量: 10768.230 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli BW25113 (大腸菌) / 参照: UniProt: P0AFX0 |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 タイプ: RIBOSOME 詳細: single particle cryo-electron microscopy structures of hibernating 100S particles isolated from stationary phase E. coli cells Entity ID: all / 由来: NATURAL |
---|---|
由来(天然) | 生物種: Escherichia coli BW25113 (大腸菌) |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R2/1 |
急速凍結 | 凍結剤: ETHANE-PROPANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 1.15 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 7.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 18000 / 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | |||||||||||||||||||||
原子モデル構築 | PDB-ID: 6H4N |