+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11426 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Uncoupled E. coli expressome, state 2 | ||||||||||||||||||
マップデータ | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides, state 2 of 6: composite map. See state 1 for focused refinement maps used to make composite. | ||||||||||||||||||
試料 |
| ||||||||||||||||||
キーワード | Transcription / Translation / Expressome / Ribosome / RNA polymerase / GENE REGULATION | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / nitrate assimilation / DNA-directed RNA polymerase complex / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / ribosomal large subunit assembly / transcription antitermination / DNA-templated transcription initiation / response to reactive oxygen species / cell motility / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosome binding / 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 / response to heat / cytosolic small ribosomal subunit / protein-containing complex assembly / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / protein dimerization activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Escherichia coli (大腸菌) / synthetic construct (人工物) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.0 Å | ||||||||||||||||||
データ登録者 | Webster MW / Takacs M | ||||||||||||||||||
資金援助 | フランス, 5件
| ||||||||||||||||||
引用 | ジャーナル: Science / 年: 2020 タイトル: Structural basis of transcription-translation coupling and collision in bacteria. 著者: Michael William Webster / Maria Takacs / Chengjin Zhu / Vita Vidmar / Ayesha Eduljee / Mo'men Abdelkareem / Albert Weixlbaumer / 要旨: Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The ...Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study. | ||||||||||||||||||
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_11426.map.gz | 304.8 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-11426-v30.xml emd-11426.xml | 102.1 KB 102.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11426_fsc.xml | 18.3 KB | 表示 | FSCデータファイル |
画像 | emd_11426.png | 93.1 KB | ||
Filedesc metadata | emd-11426.cif.gz | 18.2 KB | ||
その他 | emd_11426_additional_1.map.gz emd_11426_additional_2.map.gz emd_11426_additional_3.map.gz emd_11426_additional_4.map.gz emd_11426_half_map_1.map.gz emd_11426_half_map_2.map.gz | 434.7 MB 279.9 MB 435.1 MB 373 MB 435.1 MB 433.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11426 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11426 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11426_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_11426_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_11426_validation.xml.gz | 26.5 KB | 表示 | |
CIF形式データ | emd_11426_validation.cif.gz | 35.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11426 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11426 | 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_11426.map.gz / 形式: CCP4 / 大きさ: 536.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides, state 2 of 6: composite map. See state 1 for focused refinement maps used to make composite. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.052 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: Uncoupled E. coli expressome with intervening mRNA length...
ファイル | emd_11426_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides, state 2 of 6: half map 2 of expressome refinement. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: Uncoupled E. coli expressome with intervening mRNA length...
ファイル | emd_11426_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides, state 2 of 6: composite map with local density sharpening. See state 1 for focused refinement maps used to make composite. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: Uncoupled E. coli expressome with intervening mRNA length...
ファイル | emd_11426_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides, state 2 of 6: half map 2 of expressome refinement. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: Uncoupled E. coli expressome with intervening mRNA length...
ファイル | emd_11426_additional_4.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides, state 2 of 6: expressome map non-composite, low-pass filtered to 8 Angstroms. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Uncoupled E. coli expressome with intervening mRNA length...
ファイル | emd_11426_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides: half map 2 of focused refinement (70S masked). | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Uncoupled E. coli expressome with intervening mRNA length...
ファイル | emd_11426_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Uncoupled E. coli expressome with intervening mRNA length 38 nucleotides: half map 1 of focused refinement (70S masked). | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Uncoupled E. coli expressome, state 2
+超分子 #1: Uncoupled E. coli expressome, state 2
+超分子 #2: 70S ribosome within the uncoupled E. coli expressome, state 2
+超分子 #3: DNA-directed RNA polymerase within the uncoupled E. coli expresso...
+超分子 #4: synthetic mRNA and template DNA
+分子 #1: 16S ribosomal RNA
+分子 #22: mRNA
+分子 #23: tRNA(fmet) P-site
+分子 #24: Phe-NH-tRNA(Phe) A-site
+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 L9
+分子 #33: 50S ribosomal protein L13
+分子 #34: 50S ribosomal protein L14
+分子 #35: 50S ribosomal protein L15
+分子 #36: 50S ribosomal protein L16
+分子 #37: 50S ribosomal protein L17
+分子 #38: 50S ribosomal protein L18
+分子 #39: 50S ribosomal protein L19
+分子 #40: 50S ribosomal protein L20
+分子 #41: 50S ribosomal protein L21
+分子 #42: 50S ribosomal protein L22
+分子 #43: 50S ribosomal protein L23
+分子 #44: 50S ribosomal protein L24
+分子 #45: 50S ribosomal protein L25
+分子 #46: 50S ribosomal protein L27
+分子 #47: 50S ribosomal protein L28
+分子 #48: 50S ribosomal protein L29
+分子 #49: 50S ribosomal protein L30
+分子 #50: 50S ribosomal protein L32
+分子 #51: 50S ribosomal protein L33
+分子 #52: 50S ribosomal protein L34
+分子 #53: 50S ribosomal protein L35
+分子 #54: 50S ribosomal protein L36
+分子 #55: 50S ribosomal protein L31
+分子 #58: DNA-directed RNA polymerase subunit alpha
+分子 #59: DNA-directed RNA polymerase subunit beta
+分子 #60: DNA-directed RNA polymerase subunit beta'
+分子 #61: DNA-directed RNA polymerase subunit omega
+分子 #56: Non-template DNA strand
+分子 #57: Template DNA strand
+分子 #62: MAGNESIUM ION
+分子 #63: PHENYLALANINE
+分子 #64: ZINC 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
緩衝液 | pH: 8 構成要素:
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: AIR | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 283 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) 検出モード: COUNTING / 平均電子線量: 42.0 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): 3.5 µm 最小 デフォーカス(公称値): 0.7000000000000001 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 |