+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21421 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | 70S ribosome bound to HIV frameshifting stem-loop (FSS) and P-site tRNA (non-rotated conformation, Structure I) | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 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 ...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 / 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 / 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 | Homo sapiens (ヒト) / Escherichia coli (大腸菌) / Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
データ登録者 | Loerch S / Bao C / Ling C / Korostelev AA / Grigorieff N / Ermolenko DM | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: Elife / 年: 2020 タイトル: mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding. 著者: Chen Bao / Sarah Loerch / Clarence Ling / Andrei A Korostelev / Nikolaus Grigorieff / Dmitri N Ermolenko / 要旨: Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via ...Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from mRNA and the transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation. | |||||||||
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_21421.map.gz | 962.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-21421-v30.xml emd-21421.xml | 62.1 KB 62.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_21421_fsc.xml | 23.9 KB | 表示 | FSCデータファイル |
画像 | emd_21421.png | 108.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21421 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21421 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_21421_validation.pdf.gz | 650.2 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_21421_full_validation.pdf.gz | 649.7 KB | 表示 | |
XML形式データ | emd_21421_validation.xml.gz | 19.1 KB | 表示 | |
CIF形式データ | emd_21421_validation.cif.gz | 26.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21421 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21421 | 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_21421.map.gz / 形式: CCP4 / 大きさ: 1 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.01 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
-試料の構成要素
+全体 : 70S ribosome bound to HIV frameshifting stem-loop (FSS) and P/E t...
+超分子 #1: 70S ribosome bound to HIV frameshifting stem-loop (FSS) and P/E t...
+分子 #1: 5S ribosomal RNA
+分子 #2: tRNAPhe
+分子 #31: 23S ribosomal RNA
+分子 #52: 16S ribosomal RNA
+分子 #53: HIV frameshift stimulating sequence mRNA
+分子 #3: 50S ribosomal protein L2
+分子 #4: 50S ribosomal protein L3
+分子 #5: 50S ribosomal protein L4
+分子 #6: 50S ribosomal protein L5
+分子 #7: 50S ribosomal protein L6
+分子 #8: 50S ribosomal protein L9
+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 #32: 30S ribosomal protein S2
+分子 #33: 30S ribosomal protein S3
+分子 #34: 30S ribosomal protein S4
+分子 #35: 30S ribosomal protein S5
+分子 #36: 30S ribosomal protein S6
+分子 #37: 30S ribosomal protein S7
+分子 #38: 30S ribosomal protein S8
+分子 #39: 30S ribosomal protein S9
+分子 #40: 30S ribosomal protein S10
+分子 #41: 30S ribosomal protein S11
+分子 #42: 30S ribosomal protein S12
+分子 #43: 30S ribosomal protein S13
+分子 #44: 30S ribosomal protein S14
+分子 #45: 30S ribosomal protein S15
+分子 #46: 30S ribosomal protein S16
+分子 #47: 30S ribosomal protein S17
+分子 #48: 30S ribosomal protein S18
+分子 #49: 30S ribosomal protein S19
+分子 #50: 30S ribosomal protein S20
+分子 #51: 30S ribosomal protein S21
+分子 #54: MAGNESIUM ION
-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
濃度 | 0.6 mg/mL |
---|---|
緩衝液 | pH: 7.5 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 298 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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: 75.0 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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.5 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |