+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5nss | |||||||||
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タイトル | Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex | |||||||||
要素 |
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キーワード | TRANSCRIPTION / transcription initiation / transcription intermediate complex / RNA polymerase / sigma54 | |||||||||
機能・相同性 | 機能・相同性情報 regulation of cellular response to stress / nitrogen fixation / DNA-binding transcription activator 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 / sigma factor activity / phosphorelay signal transduction system ...regulation of cellular response to stress / nitrogen fixation / DNA-binding transcription activator 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 / sigma factor activity / phosphorelay signal transduction system / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / transcription regulator complex / sequence-specific DNA binding / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli K-12 (大腸菌) Klebsiella pneumoniae (肺炎桿菌) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.8 Å | |||||||||
データ登録者 | Glyde, R. / Ye, F.Z. / Darbari, V.C. / Zhang, N. / Buck, M. / Zhang, X.D. | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Mol Cell / 年: 2017 タイトル: Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. 著者: Robert Glyde / Fuzhou Ye / Vidya Chandran Darbari / Nan Zhang / Martin Buck / Xiaodong Zhang / 要旨: Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex ...Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. | |||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5nss.cif.gz | 903.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5nss.ent.gz | 667.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5nss.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 5nss_validation.pdf.gz | 806.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5nss_full_validation.pdf.gz | 879.2 KB | 表示 | |
XML形式データ | 5nss_validation.xml.gz | 119.9 KB | 表示 | |
CIF形式データ | 5nss_validation.cif.gz | 192.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ns/5nss ftp://data.pdbj.org/pub/pdb/validation_reports/ns/5nss | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
-DNA-directed RNA polymerase subunit ... , 4種, 5分子 ABCDE
#1: タンパク質 | 分子量: 36558.680 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: rpoA, pez, phs, sez, b3295, JW3257 / プラスミド: pGEM / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Gold pLysS AG / 参照: UniProt: P0A7Z4, DNA-directed RNA polymerase #2: タンパク質 | | 分子量: 150820.875 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) 遺伝子: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 プラスミド: pET28b+ / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Gold pLysS AG / 参照: UniProt: P0A8V2, DNA-directed RNA polymerase #3: タンパク質 | | 分子量: 158941.062 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: rpoC, tabB, b3988, JW3951 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Gold pLysS AG / 参照: UniProt: P0A8T7, DNA-directed RNA polymerase #4: タンパク質 | | 分子量: 10249.547 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: rpoZ, b3649, JW3624 / プラスミド: pGEM / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Gold pLysS AG / 参照: UniProt: P0A800, DNA-directed RNA polymerase |
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-タンパク質 , 2種, 7分子 FGJKLNM
#5: タンパク質 | 分子量: 33187.777 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: pspF, ycjB, b1303, JW1296 / プラスミド: pGEM / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Gold pLysS AG / 参照: UniProt: P37344 #7: タンパク質 | | |
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