+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22469 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | 70S ribosome stalled on long mRNA with ArfB bound in the A site | |||||||||
マップデータ | Refinement map of 3.5 Angstrom was blocfiltered with no B factor applied. | |||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / 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 ...translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / 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 / rescue of stalled ribosome / DnaA-L2 complex / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / response to reactive oxygen species / DNA endonuclease activity / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / リボソーム生合成 / regulation of translation / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / 生体膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | 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: 3.5 Å | |||||||||
データ登録者 | Carbone CE / Korostelev AA | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: ArfB can displace mRNA to rescue stalled ribosomes. 著者: Christine E Carbone / Gabriel Demo / Rohini Madireddy / Egor Svidritskiy / Andrei A Korostelev / 要旨: Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ...Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_22469.map.gz | 15.3 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-22469-v30.xml emd-22469.xml | 69.4 KB 69.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_22469.png | 188.4 KB | ||
その他 | emd_22469_additional_1.map.gz emd_22469_half_map_1.map.gz emd_22469_half_map_2.map.gz | 164.8 MB 83.8 MB 83.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22469 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22469 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_22469.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Refinement map of 3.5 Angstrom was blocfiltered with no B factor applied. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.042 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: Original 3.5 Angstrom map with no B factor applied.
ファイル | emd_22469_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Original 3.5 Angstrom map with no B factor applied. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: half map 1
ファイル | emd_22469_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | half map 1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: half map 2
ファイル | emd_22469_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | half map 2 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : 70S ribosome stalled on long mRNA with ArfB bound in the A site
+超分子 #1: 70S ribosome stalled on long mRNA with ArfB bound in the A site
+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 L13
+分子 #9: 50S ribosomal protein L14
+分子 #10: 50S ribosomal protein L15
+分子 #11: 50S ribosomal protein L16
+分子 #12: 50S ribosomal protein L17
+分子 #13: 50S ribosomal protein L18
+分子 #14: 50S ribosomal protein L19
+分子 #15: 50S ribosomal protein L20
+分子 #16: 50S ribosomal protein L21
+分子 #17: 50S ribosomal protein L22
+分子 #18: 50S ribosomal protein L23
+分子 #19: 50S ribosomal protein L24
+分子 #20: 50S ribosomal protein L25
+分子 #21: 50S ribosomal protein L27
+分子 #22: 50S ribosomal protein L28
+分子 #23: 50S ribosomal protein L29
+分子 #24: 50S ribosomal protein L30
+分子 #25: 50S ribosomal protein L32
+分子 #26: 50S ribosomal protein L33
+分子 #27: 50S ribosomal protein L34
+分子 #28: 50S ribosomal protein L35
+分子 #29: 50S ribosomal protein L36
+分子 #30: 30S ribosomal protein S2
+分子 #31: 30S ribosomal protein S3
+分子 #32: 30S ribosomal protein S4
+分子 #33: 30S ribosomal protein S5
+分子 #34: 30S ribosomal protein S6
+分子 #35: 30S ribosomal protein S7
+分子 #36: 30S ribosomal protein S8
+分子 #37: 30S ribosomal protein S9
+分子 #38: 30S ribosomal protein S10
+分子 #39: 30S ribosomal protein S11
+分子 #40: 30S ribosomal protein S12
+分子 #41: 30S ribosomal protein S13
+分子 #42: 30S ribosomal protein S14
+分子 #43: 30S ribosomal protein S15
+分子 #44: 30S ribosomal protein S16
+分子 #45: 30S ribosomal protein S17
+分子 #46: 30S ribosomal protein S18
+分子 #47: 30S ribosomal protein S19
+分子 #48: 30S ribosomal protein S20
+分子 #49: 30S ribosomal protein S21
+分子 #55: Peptidyl-tRNA hydrolase ArfB
+分子 #50: 16S ribosomal RNA
+分子 #51: 23S ribosomal RNA
+分子 #52: 5S ribosomal RNA
+分子 #53: tRNAfMet
+分子 #54: mRNA
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
---|---|
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 FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 49.6 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: Ab initio |
---|---|
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 8184 |