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Open data
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Basic information
Entry | Database: PDB / ID: 2ja6 | |||||||||
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Title | CPD lesion containing RNA Polymerase II elongation complex B | |||||||||
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![]() | TRANSFERASE / DNA-DIRECTED RNA POLYMERASE / LESION RECOGNITION / TRANSFERASE/DNA/RNA / DNA DAMAGE / ZINC-FINGER / DNA-BINDING / PHOTOLESION / PHOSPHORYLATION / MISINCORPORATION / RNA POLYMERASE II / TRANSCRIPTION- COUPLED REPAIR / TCR / CPD / ZINC / ARREST / STALLING / DNA LESION / METAL-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION BUBBLE / NUCLEOTIDYLTRANSFERASE / DAMAGE RECOGNITION / ELONGATION COMPLEX / THYMINE DIMER / TRANSCRIPTION / CYCLOBUTANE PYRIMIDINE DIMER | |||||||||
Function / homology | ![]() 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 / 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 II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / translation initiation factor binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Brueckner, F. / Hennecke, U. / Carell, T. / Cramer, P. | |||||||||
![]() | ![]() Title: CPD damage recognition by transcribing RNA polymerase II. Authors: Brueckner, F. / Hennecke, U. / Carell, T. / Cramer, P. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 831.8 KB | Display | ![]() |
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PDB format | ![]() | 653.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 535.8 KB | Display | ![]() |
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Full document | ![]() | 869.4 KB | Display | |
Data in XML | ![]() | 122.5 KB | Display | |
Data in CIF | ![]() | 178.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ja5C ![]() 2ja7C ![]() 2ja8C ![]() 1y1wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA-DIRECTED RNA POLYMERASE II ... , 7 types, 7 molecules ABCDGIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / 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 / 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 / References: UniProt: P16370, DNA-directed RNA polymerase |
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P20433, DNA-directed RNA polymerase |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / 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 / 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 / References: UniProt: P38902, DNA-directed RNA polymerase |
-DNA-DIRECTED RNA POLYMERASES I, II, AND III ... , 4 types, 4 molecules EFHL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P20434, DNA-directed RNA polymerase |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / 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 / References: UniProt: P20436, 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 / References: UniProt: P40422, DNA-directed RNA polymerase |
-DNA chain , 2 types, 2 molecules NT
#13: DNA chain | Mass: 4294.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others) |
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#15: DNA chain | Mass: 7934.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 2 molecules JP
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P22139, DNA-directed RNA polymerase |
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#14: RNA chain | Mass: 3506.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 9 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#16: Chemical | ChemComp-MG / |
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#17: Chemical | ChemComp-ZN / |
-Details
Nonpolymer details | TT: THYMINE-THYMINE CYCLOBUTAN |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.96 Å3/Da / Density % sol: 82.18 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 104987 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Y1W Resolution: 4→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 133.7 Å2 / ksol: 0.424048 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 4→50 Å
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Refine LS restraints |
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