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万見- EMDB-25407: Mid translocation intermediate with EF-G bound with GDP (Structure IV) -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25407 | |||||||||||||||
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タイトル | Mid translocation intermediate with EF-G bound with GDP (Structure IV) | |||||||||||||||
マップデータ | main map for refinement; blocfiltered and sharpened to -50 at 3.3A | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / mRNA base-pairing translational repressor activity / 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 / translation elongation factor activity / 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 / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / 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 / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||||||||
生物種 | Escherichia coli K-12 (大腸菌) / Escherichia coli 113303 (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: 3.3 Å | |||||||||||||||
データ登録者 | Carbone CE / Korostelev AA | |||||||||||||||
資金援助 | チェコ, 4件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. 著者: Christine E Carbone / Anna B Loveland / Howard B Gamper / Ya-Ming Hou / Gabriel Demo / Andrei A Korostelev / 要旨: During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that ...During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation. | |||||||||||||||
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_25407.map.gz | 320.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25407-v30.xml emd-25407.xml | 78.3 KB 78.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25407.png | 192.8 KB | ||
その他 | emd_25407_additional_1.map.gz emd_25407_additional_2.map.gz emd_25407_additional_3.map.gz emd_25407_half_map_1.map.gz emd_25407_half_map_2.map.gz | 317.5 MB 320.7 MB 317.5 MB 167.3 MB 167.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25407 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25407 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25407_validation.pdf.gz | 799.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25407_full_validation.pdf.gz | 799.4 KB | 表示 | |
XML形式データ | emd_25407_validation.xml.gz | 17.7 KB | 表示 | |
CIF形式データ | emd_25407_validation.cif.gz | 20.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25407 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25407 | 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_25407.map.gz / 形式: CCP4 / 大きさ: 343 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | main map for refinement; blocfiltered and sharpened to -50 at 3.3A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.8271 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
-追加マップ: main map for refinement without filtering or sharpening.
ファイル | emd_25407_additional_1.map | ||||||||||||
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注釈 | main map for refinement without filtering or sharpening. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: map isolated by gtpase masking. Used in modeling...
ファイル | emd_25407_additional_2.map | ||||||||||||
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注釈 | map isolated by gtpase masking. Used in modeling and local refinement of EF-G's gtpase center. Blocfiltered and sharpened to -50 at 3.25A. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: map isolated by gtpase masking without filtering or sharpening.
ファイル | emd_25407_additional_3.map | ||||||||||||
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注釈 | map isolated by gtpase masking without filtering or sharpening. | ||||||||||||
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
ファイル | emd_25407_half_map_1.map | ||||||||||||
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注釈 | half map 1 | ||||||||||||
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
ファイル | emd_25407_half_map_2.map | ||||||||||||
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注釈 | half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Mid translocation intermediate with EF-G bound with GDP (Structure IV)
+超分子 #1: Mid translocation intermediate with EF-G bound with GDP (Structure IV)
+分子 #1: 16S rRNA
+分子 #2: 23S rRNA
+分子 #3: 5S RNA
+分子 #5: tRNA fMet
+分子 #37: mRNA
+分子 #38: tRNA Pro
+分子 #4: Elongation factor G
+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 L1
+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 #39: 30S ribosomal protein S2
+分子 #40: 30S ribosomal protein S3
+分子 #41: 30S ribosomal protein S4
+分子 #42: 30S ribosomal protein S5
+分子 #43: 30S ribosomal protein S6
+分子 #44: 30S ribosomal protein S7
+分子 #45: 30S ribosomal protein S8
+分子 #46: 30S ribosomal protein S9
+分子 #47: 30S ribosomal protein S10
+分子 #48: 30S ribosomal protein S11
+分子 #49: 30S ribosomal protein S12
+分子 #50: 30S ribosomal protein S13
+分子 #51: 30S ribosomal protein S14
+分子 #52: 30S ribosomal protein S15
+分子 #53: 30S ribosomal protein S16
+分子 #54: 30S ribosomal protein S17
+分子 #55: 30S ribosomal protein S18
+分子 #56: 30S ribosomal protein S19
+分子 #57: 30S ribosomal protein S20
+分子 #58: 30S ribosomal protein S21
+分子 #59: GUANOSINE-5'-DIPHOSPHATE
-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: 7.5 |
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凍結 | 凍結剤: ETHANE |
-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 K3 (6k x 4k) / 平均電子線量: 47.6 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 / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |