+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30598 | ||||||||||||
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タイトル | Cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor | ||||||||||||
マップデータ | Cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase and trigger factor | ||||||||||||
試料 |
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キーワード | Escherichia coli / ribosome / nascent chain / protein biogenesis / peptide deformylase / trigger factor | ||||||||||||
機能・相同性 | 機能・相同性情報 'de novo' cotranslational protein folding / co-translational protein modification / stress response to copper ion / peptide deformylase / peptide deformylase activity / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding ...'de novo' cotranslational protein folding / co-translational protein modification / stress response to copper ion / peptide deformylase / peptide deformylase activity / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / protein unfolding / 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 / translational termination / DnaA-L2 complex / translation repressor activity / chaperone-mediated protein folding / negative regulation of DNA-templated DNA replication initiation / negative regulation of translational initiation / protein folding chaperone / 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 / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ferrous iron binding / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / protein transport / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / response to heat / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / hydrolase activity / ribosome / structural constituent of ribosome / translation / cell division / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | Escherichia coli (大腸菌) / Escherichia coli (strain K12) (大腸菌) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | ||||||||||||
データ登録者 | Akbar S / Bhakta S | ||||||||||||
資金援助 | インド, 3件
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引用 | ジャーナル: Structure / 年: 2021 タイトル: Structural insights into the interplay of protein biogenesis factors with the 70S ribosome. 著者: Shirin Akbar / Sayan Bhakta / Jayati Sengupta / 要旨: Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase ...Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance. Here, we present two high-resolution cryoelectron microscopy structures of tRNA-bound E. coli ribosome complexes showing simultaneous binding of PDF and TF, in the absence (3.4 Å) and presence of MetAP (4.1 Å). These structures establish molecular details of the interactions of the factors with the ribosome, and thereby reveal the structural basis of nascent chain processing. Our results suggest that simultaneous binding of all three factors is not a functionally favorable mechanism of nascent chain processing. Strikingly, an unusual structural distortion of the 70S ribosome, potentially driven by binding of multiple copies of MetAP, is observed when MetAP is incubated with a pre-formed PDF-TF-bound ribosome complex. | ||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_30598.map.gz | 111.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30598-v30.xml emd-30598.xml | 71 KB 71 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_30598_fsc.xml | 14.5 KB | 表示 | FSCデータファイル |
画像 | emd_30598.png | 191.2 KB | ||
Filedesc metadata | emd-30598.cif.gz | 14.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30598 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30598 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30598_validation.pdf.gz | 603 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30598_full_validation.pdf.gz | 602.6 KB | 表示 | |
XML形式データ | emd_30598_validation.xml.gz | 12.8 KB | 表示 | |
CIF形式データ | emd_30598_validation.cif.gz | 17 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30598 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30598 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_30598.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase and trigger factor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : E. coli 70S ribosome in complex with enzyme peptide deformylase a...
+超分子 #1: E. coli 70S ribosome in complex with enzyme peptide deformylase a...
+分子 #1: 30S ribosomal protein S20
+分子 #2: 30S ribosomal protein S21
+分子 #6: 50S ribosomal protein L31
+分子 #9: 50S ribosomal protein L2
+分子 #10: 50S ribosomal protein L3
+分子 #11: 50S ribosomal protein L4
+分子 #12: 50S ribosomal protein L5
+分子 #13: 50S ribosomal protein L6
+分子 #14: 50S ribosomal protein L9
+分子 #15: 50S ribosomal protein L11
+分子 #16: 50S ribosomal protein L13
+分子 #17: 50S ribosomal protein L14
+分子 #18: 50S ribosomal protein L15
+分子 #19: 50S ribosomal protein L16
+分子 #20: 50S ribosomal protein L17
+分子 #21: 50S ribosomal protein L18
+分子 #22: 50S ribosomal protein L19
+分子 #23: 50S ribosomal protein L20
+分子 #24: 50S ribosomal protein L21
+分子 #25: 50S ribosomal protein L22
+分子 #26: 50S ribosomal protein L30
+分子 #27: 50S ribosomal protein L24
+分子 #28: 50S ribosomal protein L25
+分子 #29: 50S ribosomal protein L27
+分子 #30: 50S ribosomal protein L28
+分子 #31: 50S ribosomal protein L29
+分子 #32: 50S ribosomal protein L23
+分子 #33: 50S ribosomal protein L32
+分子 #34: 50S ribosomal protein L33
+分子 #35: 50S ribosomal protein L34
+分子 #36: 50S ribosomal protein L35
+分子 #37: 50S ribosomal protein L36
+分子 #39: Peptide deformylase
+分子 #40: Trigger factor
+分子 #41: 30S ribosomal protein S2
+分子 #42: 30S ribosomal protein S3
+分子 #43: 30S ribosomal protein S4
+分子 #44: 30S ribosomal protein S5
+分子 #45: 30S ribosomal protein S6, fully modified isoform
+分子 #46: 30S ribosomal protein S7
+分子 #47: 30S ribosomal protein S8
+分子 #48: 30S ribosomal protein S9
+分子 #49: 30S ribosomal protein S10
+分子 #50: 30S ribosomal protein S11
+分子 #51: 30S ribosomal protein S12
+分子 #52: 30S ribosomal protein S13
+分子 #53: 30S ribosomal protein S14
+分子 #54: 30S ribosomal protein S15
+分子 #55: 30S ribosomal protein S16
+分子 #56: 30S ribosomal protein S17
+分子 #57: 30S ribosomal protein S18
+分子 #58: 30S ribosomal protein S19
+分子 #3: E-site tRNA
+分子 #4: P-site tRNA
+分子 #5: A-site tRNA
+分子 #7: 23S ribosomal rRNA
+分子 #8: 5S ribosomal rRNA
+分子 #38: 16S ribosomal rRNA
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.4 |
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グリッド | モデル: Quantifoil / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY ARRAY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 平均電子線量: 32.57 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |