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基本情報
登録情報 | データベース: EMDB / ID: EMD-21635 | ||||||||||||
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タイトル | Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure VI-B) | ||||||||||||
![]() | Map VI-B blocfilt filtered and with B-factor -50 applied | ||||||||||||
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![]() | Ribosome / EF-Tu / tRNA | ||||||||||||
機能・相同性 | ![]() 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 ...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 / translational termination / DnaA-L2 complex / four-way junction DNA binding / 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 / transcription antitermination / response to reactive oxygen species / regulation of cell growth / ribosomal large subunit assembly / 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 | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | ||||||||||||
![]() | Loveland AB / Demo G | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. 著者: Anna B Loveland / Gabriel Demo / Andrei A Korostelev / ![]() ![]() 要旨: Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary ...Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge. Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states and in proofreading states, which together govern the efficient rejection of incorrect tRNA. | ||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 85.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 77.7 KB 77.7 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 9.9 KB | 表示 | ![]() |
画像 | ![]() | 143.8 KB | ||
Filedesc metadata | ![]() | 13.5 KB | ||
その他 | ![]() ![]() ![]() | 84.5 MB 34 MB 34 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6wdgMC ![]() 6wd0C ![]() 6wd1C ![]() 6wd2C ![]() 6wd3C ![]() 6wd4C ![]() 6wd5C ![]() 6wd6C ![]() 6wd7C ![]() 6wd8C ![]() 6wd9C ![]() 6wdaC ![]() 6wdbC ![]() 6wdcC ![]() 6wddC ![]() 6wdeC ![]() 6wdfC ![]() 6wdhC ![]() 6wdiC ![]() 6wdjC ![]() 6wdkC ![]() 6wdlC ![]() 6wdmC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Map VI-B blocfilt filtered and with B-factor -50 applied | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.333 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-追加マップ: Map VI-B
ファイル | emd_21635_additional.map | ||||||||||||
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注釈 | Map VI-B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2 VI-B
ファイル | emd_21635_half_map_1.map | ||||||||||||
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注釈 | Half map 2 VI-B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1 VI-B
ファイル | emd_21635_half_map_2.map | ||||||||||||
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注釈 | Half map 1 VI-B | ||||||||||||
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密度ヒストグラム |
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試料の構成要素
+全体 : Map VI-B
+超分子 #1: Map VI-B
+分子 #1: 50S ribosomal protein L2
+分子 #2: 50S ribosomal protein L3
+分子 #3: 50S ribosomal protein L4
+分子 #4: 50S ribosomal protein L5
+分子 #5: 50S ribosomal protein L6
+分子 #6: 50S ribosomal protein L9
+分子 #7: 50S ribosomal protein L10
+分子 #8: 50S ribosomal protein L11
+分子 #9: 50S ribosomal protein L13
+分子 #10: 50S ribosomal protein L14
+分子 #11: 50S ribosomal protein L15
+分子 #12: 50S ribosomal protein L16
+分子 #13: 50S ribosomal protein L17
+分子 #14: 50S ribosomal protein L18
+分子 #15: 50S ribosomal protein L19
+分子 #16: 50S ribosomal protein L20
+分子 #17: 50S ribosomal protein L21
+分子 #18: 50S ribosomal protein L22
+分子 #19: 50S ribosomal protein L23
+分子 #20: 50S ribosomal protein L24
+分子 #21: 50S ribosomal protein L25
+分子 #22: 50S ribosomal protein L27
+分子 #23: 50S ribosomal protein L28
+分子 #24: 50S ribosomal protein L29
+分子 #25: 50S ribosomal protein L30
+分子 #26: 50S ribosomal protein L32
+分子 #27: 50S ribosomal protein L33
+分子 #28: 50S ribosomal protein L34
+分子 #29: 50S ribosomal protein L35
+分子 #30: 50S ribosomal protein L36
+分子 #31: 30S ribosomal protein S2
+分子 #32: 30S ribosomal protein S3
+分子 #33: 30S ribosomal protein S4
+分子 #34: 30S ribosomal protein S5
+分子 #35: 30S ribosomal protein S6
+分子 #36: 30S ribosomal protein S7
+分子 #37: 30S ribosomal protein S8
+分子 #38: 30S ribosomal protein S9
+分子 #39: 30S ribosomal protein S10
+分子 #40: 30S ribosomal protein S11
+分子 #41: 30S ribosomal protein S12
+分子 #42: 30S ribosomal protein S13
+分子 #43: 30S ribosomal protein S14
+分子 #44: 30S ribosomal protein S15
+分子 #45: 30S ribosomal protein S16
+分子 #46: 30S ribosomal protein S17
+分子 #47: 30S ribosomal protein S18
+分子 #48: 30S ribosomal protein S19
+分子 #49: 30S ribosomal protein S20
+分子 #50: 30S ribosomal protein S21
+分子 #51: 50S ribosomal protein L1
+分子 #52: 16S ribosomal RNA
+分子 #53: 23S ribosomal RNA
+分子 #54: 5S ribosomal RNA
+分子 #55: tRNAfMet
+分子 #56: mRNA
+分子 #57: tRNAPhe
+分子 #58: PHENYLALANINE
+分子 #59: N-FORMYLMETHIONINE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
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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: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - 画像ごとのフレーム数: 1-35 / 撮影したグリッド数: 1 / 実像数: 3218 / 平均露光時間: 1.0 sec. / 平均電子線量: 35.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
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 |
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画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT / 当てはまり具合の基準: Correlation coefficient |
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得られたモデル | ![]() PDB-6wdg: |