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- PDB-8s5n: RNA polymerase II core initially transcribing complex with an ord... -
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Basic information
Entry | Database: PDB / ID: 8s5n | ||||||
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Title | RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt | ||||||
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![]() | TRANSCRIPTION / RNA polymerase II / promoter escape / de novo transcription | ||||||
Function / homology | ![]() positive regulation of core promoter binding / meiotic sister chromatid cohesion / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / 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 ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / 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 / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / 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 / 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 Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / germinal vesicle / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / protein acetylation / : / : / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / cell division site / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / viral transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / organelle membrane / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / acetyltransferase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / spindle assembly / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | 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. | ||||||
History |
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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 | ![]() | 817.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 136.6 KB | Display | |
Data in CIF | ![]() | 216 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19743MC ![]() 8s51C ![]() 8s52C ![]() 8s54C ![]() 8s55C 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: 218889.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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: 3769.344 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: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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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: NO / Vitrification applied: YES | ||||||||||||||||||
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 / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm |
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18827 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 142.72 Å2 | ||||||||||||||||||||||||
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