+Open data
-Basic information
Entry | Database: PDB / ID: 1i50 | ||||||
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Title | RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION | ||||||
Components | (DNA-DIRECTED RNA POLYMERASE II ...Polymerase) x 10 | ||||||
Keywords | TRANSCRIPTION / MRNA / MULTIPROTEIN COMPLEX / MOLECULAR MACHINE / ZINC MOTIFS | ||||||
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 / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å | ||||||
Authors | Cramer, P. / Bushnell, D.A. / Kornberg, R.D. | ||||||
Citation | Journal: Science / Year: 2001 Title: Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Authors: Cramer, P. / Bushnell, D.A. / Kornberg, R.D. #1: Journal: Science / Year: 2000 Title: Architecture of RNA Polymerase II and Implications for the Transcription Mechanism Authors: Cramer, P. / Bushnell, D.A. / Fu, J. / Gnatt, A.L. / Maier-Davis, B. / Thompson, N.E. / Burgess, R.R. / Edwards, A.M. / David, P.R. / Kornberg, R.D. | ||||||
History |
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Remark 650 | HELIX REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was ...HELIX REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was assigned by visual inspecition, see primary citation. | ||||||
Remark 700 | SHEET REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was ...SHEET REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was assigned by visual inspecition, see primary citation. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i50.cif.gz | 718.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i50.ent.gz | 572.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i50 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i50 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DNA-DIRECTED RNA POLYMERASE II ... , 10 types, 10 molecules ABCEFHIJKL
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P04050, DNA-directed RNA polymerase |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P08518, DNA-directed RNA polymerase |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P16370, DNA-directed RNA polymerase |
#4: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20434, DNA-directed RNA polymerase |
#5: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20435, DNA-directed RNA polymerase |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20436, DNA-directed RNA polymerase |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P27999, DNA-directed RNA polymerase |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P22139, DNA-directed RNA polymerase |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P38902, DNA-directed RNA polymerase |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P40422, DNA-directed RNA polymerase |
-Non-polymers , 3 types, 87 molecules
#11: Chemical | ChemComp-ZN / #12: Chemical | ChemComp-MN / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.07 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, AMMONIUMHYDROGENPHOSPHATE, SODIUMDIHYDROGENPHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Fu, J., (1999) Cell, 98, 799. / pH: 6.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.291 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.291 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 125251 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.344 / % possible all: 96.2 |
Reflection | *PLUS Lowest resolution: 40 Å / Redundancy: 3.6 % |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 96.2 % / Num. unique obs: 12023 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.8→40 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 64.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.229 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |