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- PDB-8s51: RNA polymerase II core initially transcribing complex with an ord... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8s51 | ||||||
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Title | RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt | ||||||
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Function / homology | ![]() positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / nuclear lumen / transcription open complex formation at RNA polymerase II promoter / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding ...positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / nuclear lumen / transcription open complex formation at RNA polymerase II promoter / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Zhan, Y. / Grabbe, F. / Oberbeckmann, E. / Dienemann, C. / Cramer, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Three-step mechanism of promoter escape by RNA polymerase II. Authors: Yumeng Zhan / Frauke Grabbe / Elisa Oberbeckmann / Christian Dienemann / Patrick Cramer / ![]() Abstract: The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how ...The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 19718MC ![]() 8s52C ![]() 8s54C ![]() 8s55C ![]() 8s5nC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEGIK
#1: Protein | ![]() Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: A0A7M4DUC2, ![]() |
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#2: Protein | ![]() Mass: 147938.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#5: Protein | ![]() Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#7: Protein | ![]() Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#9: Protein | ![]() Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#11: Protein | ![]() Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-RNA polymerase II subunit ... , 2 types, 2 molecules DL
#4: Protein | ![]() Mass: 20962.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#12: Protein | ![]() Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ
#6: Protein | ![]() Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#8: Protein | ![]() Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#10: Protein | ![]() Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Transcription initiation factor ... , 4 types, 4 molecules MUVX
#13: Protein | Mass: 34877.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#20: Protein | Mass: 41544.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#21: Protein | Mass: 12469.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#23: Protein | Mass: 33106.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 43236.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#19: DNA chain | Mass: 42569.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein , 2 types, 2 molecules OW
#15: Protein | Mass: 37729.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#22: Protein | Mass: 49516.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-RNA chain , 1 types, 1 molecules P
#16: RNA chain | ![]() Mass: 2508.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-General transcription factor IIF subunit ... , 2 types, 2 molecules QR
#17: Protein | Mass: 58343.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#18: Protein | Mass: 28427.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 2 types, 11 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#24: Chemical | ChemComp-ZN / #25: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Source (natural) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction![]() | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87097 / Symmetry type: POINT |