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Yorodumi- PDB-8s52: RNA polymerase II core initially transcribing complex with an ord... -
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-Basic information
Entry | Database: PDB / ID: 8s52 | ||||||
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Title | RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase II / promoter escape / de novo transcription | ||||||
Function / homology | Function and homology information positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / 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 / nuclear lumen / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / : / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / cell division site / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / 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 / viral transcription / acetyltransferase activity / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / organelle membrane / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) unidentified adenovirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Zhan, Y. / Grabbe, F. / Oberbeckmann, E. / Dienemann, C. / Cramer, P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Mol Cell / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s52.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8s52.ent.gz | 820.3 KB | Display | PDB format |
PDBx/mmJSON format | 8s52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/8s52 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/8s52 | HTTPS FTP |
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-Related structure data
Related structure data | 19719MC 8s51C 8s54C 8s55C 8s5nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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) Sus scrofa (pig) / 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) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase |
#3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3 |
#5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7 |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899 |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4 |
-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) Sus scrofa (pig) / References: UniProt: A0A287ADR4 |
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#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0JYF1 |
-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) Sus scrofa (pig) / References: UniProt: A0A8D1KNW4 |
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#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2 |
#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0 |
-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.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403, histone acetyltransferase |
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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.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P52655 |
#21: Protein | Mass: 12469.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P52657 |
#23: Protein | Mass: 33106.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E2, TF2E2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29084 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 43236.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus |
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#19: DNA chain | Mass: 42569.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus |
-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.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Escherichia coli (E. coli) / References: UniProt: P20226 |
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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.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083 |
-RNA chain , 1 types, 1 molecules P
#16: RNA chain | Mass: 3118.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus |
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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.) Homo sapiens (human) / Gene: GTF2F1, RAP74 / Production host: Escherichia coli (E. coli) / References: UniProt: P35269 |
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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.) Homo sapiens (human) / Gene: GTF2F2, RAP30 / Production host: Escherichia coli (E. coli) / References: UniProt: P13984, DNA helicase |
-Non-polymers , 2 types, 11 molecules
#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 |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151975 / Symmetry type: POINT |