+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4478 | |||||||||
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タイトル | Structure of tmRNA SmpB bound past E site of E. coli 70S ribosome | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | tmRNA SmpB trans-translation translation / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 trans-translation / 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 / transcriptional attenuation / endoribonuclease inhibitor activity ...trans-translation / 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 / 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 / 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 / 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 / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (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: 3.7 Å | |||||||||
データ登録者 | Rae CD | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Science / 年: 2019 タイトル: How a circularized tmRNA moves through the ribosome. 著者: Christopher D Rae / Yuliya Gordiyenko / V Ramakrishnan / 要旨: During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo- ...During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA. | |||||||||
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_4478.map.gz | 15.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4478-v30.xml emd-4478.xml | 78.3 KB 78.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4478.png | 72.2 KB | ||
Filedesc metadata | emd-4478.cif.gz | 14.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4478 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4478 | 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_4478.map.gz / 形式: CCP4 / 大きさ: 209.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.15 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 : Structure of tmRNA SmpB bound in state past E site of E. coli 70S...
+超分子 #1: Structure of tmRNA SmpB bound in state past E site of E. coli 70S...
+超分子 #2: ribosome
+超分子 #3: nascent peptide
+超分子 #4: SsrA-binding protein
+超分子 #5: tmRNA
+分子 #1: 23S ribosomal RNA
+分子 #2: 16S ribosomal RNA
+分子 #3: 5S ribosomal RNA
+分子 #5: P-site tRNA
+分子 #58: tmRNA
+分子 #4: Nascent peptide
+分子 #6: 50S ribosomal protein L2
+分子 #7: 50S ribosomal protein L3
+分子 #8: 50S ribosomal protein L4
+分子 #9: 50S ribosomal protein L5
+分子 #10: 50S ribosomal protein L6
+分子 #11: 50S ribosomal protein L9
+分子 #12: 50S ribosomal protein L10
+分子 #13: 50S ribosomal protein L11
+分子 #14: 50S ribosomal protein L13
+分子 #15: 50S ribosomal protein L14
+分子 #16: 50S ribosomal protein L15
+分子 #17: 50S ribosomal protein L16
+分子 #18: 50S ribosomal protein L17
+分子 #19: 50S ribosomal protein L18
+分子 #20: 50S ribosomal protein L19
+分子 #21: 50S ribosomal protein L20
+分子 #22: 50S ribosomal protein L21
+分子 #23: 50S ribosomal protein L22
+分子 #24: 50S ribosomal protein L23
+分子 #25: 50S ribosomal protein L24
+分子 #26: 50S ribosomal protein L25
+分子 #27: 50S ribosomal protein L27
+分子 #28: 50S ribosomal protein L28
+分子 #29: 50S ribosomal protein L29
+分子 #30: 50S ribosomal protein L30
+分子 #31: 50S ribosomal protein L31
+分子 #32: 50S ribosomal protein L32
+分子 #33: 50S ribosomal protein L33
+分子 #34: 50S ribosomal protein L34
+分子 #35: 50S ribosomal protein L35
+分子 #36: 50S ribosomal protein L36
+分子 #37: 30S ribosomal protein S2
+分子 #38: 30S ribosomal protein S3
+分子 #39: 30S ribosomal protein S4
+分子 #40: 30S ribosomal protein S5
+分子 #41: 30S ribosomal protein S6
+分子 #42: 30S ribosomal protein S7
+分子 #43: 30S ribosomal protein S8
+分子 #44: 30S ribosomal protein S9
+分子 #45: 30S ribosomal protein S10
+分子 #46: 30S ribosomal protein S11
+分子 #47: 30S ribosomal protein S12
+分子 #48: 30S ribosomal protein S13
+分子 #49: 30S ribosomal protein S14
+分子 #50: 30S ribosomal protein S15
+分子 #51: 30S ribosomal protein S16
+分子 #52: 30S ribosomal protein S17
+分子 #53: 30S ribosomal protein S18
+分子 #54: 30S ribosomal protein S19
+分子 #55: 30S ribosomal protein S20
+分子 #56: 30S ribosomal protein S21
+分子 #57: SsrA-binding protein
+分子 #59: MAGNESIUM ION
+分子 #60: ZINC ION
+分子 #61: water
-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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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 60.0 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: Tecnai Polara / 画像提供: FEI Company |