+Open data
-Basic information
Entry | Database: PDB / ID: 1nt9 | ||||||
---|---|---|---|---|---|---|---|
Title | Complete 12-subunit RNA polymerase II | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / TRANSFERASE / DNA-dependent RNA polymerase / cellular RNA polymerase / multisubunit complex / gene expression / mRNA / messenger RNA synthesis | ||||||
Function / homology | Function and homology information RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / termination of RNA polymerase II transcription / 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 / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / translation initiation factor binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / ribosome biogenesis / peroxisome / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Armache, K.-J. / Kettenberger, H. / Cramer, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Architecture of initiation-competent 12-subunit RNA polymerase II Authors: Armache, K.-J. / Kettenberger, H. / Cramer, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nt9.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nt9.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nt9_validation.pdf.gz | 381.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1nt9_full_validation.pdf.gz | 381.3 KB | Display | |
Data in XML | 1nt9_validation.xml.gz | 979 B | Display | |
Data in CIF | 1nt9_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1nt9 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1nt9 | HTTPS FTP |
-Related structure data
Related structure data | 1i6hS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-DNA-DIRECTED RNA POLYMERASE II ... , 5 types, 5 molecules ACGIK
#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 |
---|---|
#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 |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P34087, DNA-directed RNA polymerase |
#9: 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 |
#11: 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 |
-Protein , 2 types, 2 molecules BD
#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 |
---|---|
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Numbering of resiudes D10-D24 is arbitrary Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P20433, DNA-directed RNA polymerase |
-DNA-directed RNA polymerases I, II, and III ... , 5 types, 5 molecules EFHJL
#5: 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 |
---|---|
#6: 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 |
#8: 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 |
#10: 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 |
#12: 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.92 Å3/Da / Density % sol: 79.22 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 20000, ammonium sodium phosphate, sodium chloride, dioxane, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9185 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→50 Å / Num. all: 83431 / Num. obs: 83431 / % possible obs: 93.8 % / Rsym value: 0.093 |
Reflection shell | Resolution: 4.2→4.35 Å / Rmerge(I) obs: 0.363 / % possible all: 89.5 |
Reflection | *PLUS Highest resolution: 4.2 Å / Lowest resolution: 50 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS Highest resolution: 4.2 Å / % possible obs: 89.5 % / Num. unique obs: 7893 |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I6H Resolution: 4.2→50 Å / σ(F): 0 Details: Model was fitted into electron densities, no least square minimization was performed
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.2→50 Å
| ||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||
Refinement | *PLUS | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|