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Yorodumi- PDB-8u9r: STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BI... -
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Basic information
| Entry | Database: PDB / ID: 8u9r | ||||||
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| Title | STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER | ||||||
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Keywords | TRANSCRIPTION / Multiprotein complex / Free-electron laser / Molecular machine | ||||||
| Function / homology | Function and homology information: / : / : / : / : / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...: / : / : / : / : / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / positive regulation of translational initiation / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / single-stranded DNA binding / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() synthetic construct (others) | ||||||
| Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.34 Å | ||||||
Authors | Arjunan, P. / Calero, G. / Kaplan, C.D. | ||||||
| Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024Title: Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Authors: Lin, G. / Barnes, C.O. / Weiss, S. / Dutagaci, B. / Qiu, C. / Feig, M. / Song, J. / Lyubimov, A. / Cohen, A.E. / Kaplan, C.D. / Calero, G. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8u9r.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb8u9r.ent.gz | 1.3 MB | Display | PDB format |
| PDBx/mmJSON format | 8u9r.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8u9r_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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| Full document | 8u9r_full_validation.pdf.gz | 1.8 MB | Display | |
| Data in XML | 8u9r_validation.xml.gz | 170.4 KB | Display | |
| Data in CIF | 8u9r_validation.cif.gz | 219.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/8u9r ftp://data.pdbj.org/pub/pdb/validation_reports/u9/8u9r | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8u9xC ![]() 9bvtC ![]() 9bw0C C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-DNA-directed RNA polymerase II subunit ... , 6 types, 6 molecules ACDGIK
| #1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / Source: (natural) ![]() |
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| #3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Source: (natural) ![]() |
| #4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / Source: (natural) ![]() |
| #7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Source: (natural) ![]() |
| #9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Source: (natural) ![]() |
| #11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Source: (natural) ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules EFH
| #5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 Source: (natural) ![]() |
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| #6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 Source: (natural) ![]() |
| #8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 Source: (natural) ![]() |
-DNA-directed RNA polymerases II subunit ... , 2 types, 2 molecules JL
| #10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 Source: (natural) ![]() |
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| #12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 Source: (natural) ![]() |
-Protein / RNA chain / DNA chain , 3 types, 3 molecules BRT
| #13: RNA chain | Mass: 3280.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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| #14: DNA chain | Mass: 4176.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
| #2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / Source: (natural) ![]() References: UniProt: A0A6A5Q4H2, DNA-directed RNA polymerase |
-Non-polymers , 5 types, 30 molecules 








| #15: Chemical | ChemComp-ZN / #16: Chemical | ChemComp-GOL / | #17: Chemical | #18: Chemical | ChemComp-ATP / | #19: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 5.59 Å3/Da / Density % sol: 77.98 % |
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| Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 10-15 % tacsimate 100mM Hepes pH 7.5 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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| Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30505 Å |
| Detector | Type: SLAC ePix10k 2M / Detector: PIXEL / Date: Sep 8, 2018 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.30505 Å / Relative weight: 1 |
| Reflection | Resolution: 3.3→24.68 Å / Num. obs: 166660 / % possible obs: 95.85 % / Redundancy: 10.25 % / CC1/2: 0.9144 / Rmerge(I) obs: 0.6 / Net I/σ(I): 3.93 |
| Reflection shell | Resolution: 3.3→3.36 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 5833 / CC1/2: 0.59 |
| Serial crystallography sample delivery | Method: fixed target |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→19.97 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.71 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.34→19.97 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Origin x: 106.2787 Å / Origin y: 50.6464 Å / Origin z: -1.3135 Å
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| Refinement TLS group | Selection details: all |
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X-RAY DIFFRACTION
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