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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-4126 | |||||||||
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タイトル | Structure of the 70S ribosome with fMetSec-tRNASec in the hybrid pre-translocation state (H) | |||||||||
![]() | final sharpened map | |||||||||
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![]() | translation / decoding / recoding / selenocysteine / ribosome | |||||||||
機能・相同性 | ![]() 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 ...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 / cytoplasm / cytosol 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: 4.6 Å | |||||||||
![]() | Fischer N / Neumann P | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: The pathway to GTPase activation of elongation factor SelB on the ribosome. 著者: Niels Fischer / Piotr Neumann / Lars V Bock / Cristina Maracci / Zhe Wang / Alena Paleskava / Andrey L Konevega / Gunnar F Schröder / Helmut Grubmüller / Ralf Ficner / Marina V Rodnina / Holger Stark / ![]() 要旨: In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA recodes ...In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA binding by SelB and show large-scale rearrangements of Sec-tRNA. Upon initial binding of SelB-Sec-tRNA to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases. | |||||||||
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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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 71.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 73.6 KB 73.6 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 9.4 KB | 表示 | ![]() |
画像 | ![]() | 148.1 KB | ||
Filedesc metadata | ![]() | 14.6 KB | ||
その他 | ![]() ![]() | 60.1 MB 59.9 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 | ![]() 5lzfMC ![]() 4121C ![]() 4122C ![]() 4123C ![]() 4124C ![]() 4125C ![]() 5lzaC ![]() 5lzbC ![]() 5lzcC ![]() 5lzdC ![]() 5lzeC 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 | |
電子顕微鏡画像生データ | ![]() Data size: 1.0 TB Data #1: Part 1 - Unprocessed cryo-EM micrographs of E. Coli 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfMet-SECIS mRNA complexes [micrographs - single frame] Data #2: Part 2 - Unprocessed cryo-EM micrographs of E. Coli 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfMet-SECIS mRNA complex [micrographs - single frame] Data #3: ribosomeSelB_particles.mrcs - CTF corrected single particle images of E. Coli 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfMet-SECIS mRNA complex [picked particles - multiframe - processed]) |
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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 | final sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.16 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
-ハーフマップ: unfiltered half-map 1 (unprocessed)
ファイル | emd_4126_half_map_1.map | ||||||||||||
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注釈 | unfiltered half-map 1 (unprocessed) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: unfiltered half-map 2 (unprocessed)
ファイル | emd_4126_half_map_2.map | ||||||||||||
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注釈 | unfiltered half-map 2 (unprocessed) | ||||||||||||
投影像・断面図 |
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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 : Hybrid pre-translocation state of E. coli ribosome 70S-fMetSec-tR...
+超分子 #1: Hybrid pre-translocation state of E. coli ribosome 70S-fMetSec-tR...
+分子 #1: 16S ribosomal RNA
+分子 #22: tRNAfMet
+分子 #23: SECIS mRNA
+分子 #24: fMetSec-tRNASec
+分子 #25: 23S ribosomal RNA
+分子 #26: 5S ribosomal RNA
+分子 #2: 30S ribosomal protein S2
+分子 #3: 30S ribosomal protein S3
+分子 #4: 30S ribosomal protein S4
+分子 #5: 30S ribosomal protein S5
+分子 #6: 30S ribosomal protein S6
+分子 #7: 30S ribosomal protein S7
+分子 #8: 30S ribosomal protein S8
+分子 #9: 30S ribosomal protein S9
+分子 #10: 30S ribosomal protein S10
+分子 #11: 30S ribosomal protein S11
+分子 #12: 30S ribosomal protein S12
+分子 #13: 30S ribosomal protein S13
+分子 #14: 30S ribosomal protein S14
+分子 #15: 30S ribosomal protein S15
+分子 #16: 30S ribosomal protein S16
+分子 #17: 30S ribosomal protein S17
+分子 #18: 30S ribosomal protein S18
+分子 #19: 30S ribosomal protein S19
+分子 #20: 30S ribosomal protein S20
+分子 #21: 30S ribosomal protein S21
+分子 #27: 50S ribosomal protein L2
+分子 #28: 50S ribosomal protein L3
+分子 #29: 50S ribosomal protein L4
+分子 #30: 50S ribosomal protein L5
+分子 #31: 50S ribosomal protein L6
+分子 #32: 50S ribosomal protein L11
+分子 #33: 50S ribosomal protein L9
+分子 #34: 50S ribosomal protein L13
+分子 #35: 50S ribosomal protein L14
+分子 #36: 50S ribosomal protein L15
+分子 #37: 50S ribosomal protein L16
+分子 #38: 50S ribosomal protein L17
+分子 #39: 50S ribosomal protein L18
+分子 #40: 50S ribosomal protein L19
+分子 #41: 50S ribosomal protein L20
+分子 #42: 50S ribosomal protein L21
+分子 #43: 50S ribosomal protein L22
+分子 #44: 50S ribosomal protein L23
+分子 #45: 50S ribosomal protein L24
+分子 #46: 50S ribosomal protein L25
+分子 #47: 50S ribosomal protein L27
+分子 #48: 50S ribosomal protein L28
+分子 #49: 50S ribosomal protein L29
+分子 #50: 50S ribosomal protein L30
+分子 #51: 50S ribosomal protein L32
+分子 #52: 50S ribosomal protein L33
+分子 #53: 50S ribosomal protein L34
+分子 #54: 50S ribosomal protein L35
+分子 #55: 50S ribosomal protein L36
+分子 #56: 50S ribosomal protein L31
+分子 #57: ZINC ION
-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 詳細: 50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT |
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グリッド | モデル: Quantifoil R3.5/1 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 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 |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 球面収差補正装置: CEOS Cs-corrector |
詳細 | Using a Cs-corrector from CEOS electron optical aberrations were corrected to residual phase errors of 45degree at scattering angles of >12 to 15 mrad. |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / 撮影したグリッド数: 1 / 実像数: 12681 / 平均露光時間: 1.0 sec. / 平均電子線量: 30.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 0.001 mm / 最大 デフォーカス(公称値): 2.6 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
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
詳細 | For parts of the model exhibiting larger conformational differences and/or lower local map resolution, additional cycles of real space refinement and manual fitting were performed against experimental map filtered to lower resolution |
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精密化 | プロトコル: FLEXIBLE FIT / 当てはまり具合の基準: Maximum likelihood |
得られたモデル | ![]() PDB-5lzf: |