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Yorodumi- PDB-4c3i: Structure of 14-subunit RNA polymerase I at 3.0 A resolution, cry... -
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-Basic information
Entry | Database: PDB / ID: 4c3i | ||||||
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Title | Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100 | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information RNA polymerase III activity / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / regulation of cell size / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping ...RNA polymerase III activity / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / regulation of cell size / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 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 / 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 I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Fernandez-Tornero, C. / Moreno-Morcillo, M. / Rashid, U.J. / Taylor, N.M.I. / Ruiz, F.M. / Gruene, T. / Legrand, P. / Steuerwald, U. / Muller, C.W. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Crystal Structure of the 14-Subunit RNA Polymerase I Authors: Fernandez-Tornero, C. / Moreno-Morcillo, M. / Rashid, U.J. / Taylor, N.M.I. / Ruiz, F.M. / Gruene, T. / Legrand, P. / Steuerwald, U. / Muller, C.W. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c3i.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4c3i.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 4c3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/4c3i ftp://data.pdbj.org/pub/pdb/validation_reports/c3/4c3i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA-DIRECTED RNA POLYMERASE I SUBUNIT ... , 7 types, 7 molecules ABDGIMN
#1: Protein | Mass: 186676.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P10964, DNA-directed RNA polymerase |
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#2: Protein | Mass: 135910.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P22138, DNA-directed RNA polymerase |
#4: Protein | Mass: 14585.103 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P50106 |
#7: Protein | Mass: 36264.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P46669 |
#9: Protein | Mass: 13676.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P32529 |
#13: Protein | Mass: 46721.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: Q01080 |
#14: Protein | Mass: 26933.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P47006 |
-DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ... , 2 types, 2 molecules CK
#3: Protein | Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P07703 |
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#11: Protein | Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P28000 |
-DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P20434 |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P20435 |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P20436 |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P22139 |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG. Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P40422 |
-Non-polymers , 4 types, 12 molecules
#15: Chemical | #16: Chemical | ChemComp-ZN / #17: Chemical | ChemComp-MG / | #18: Chemical | ChemComp-MPD / ( | |
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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: 2.88 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | Details: 10% MPD, 0.1M TRIS HCL PH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2013 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 3→84 Å / Num. obs: 132738 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 89.25 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.33 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.83 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→84 Å / Cor.coef. Fo:Fc: 0.9413 / Cor.coef. Fo:Fc free: 0.9273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.998 / SU Rfree Blow DPI: 0.336 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=34244. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=34244. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
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Displacement parameters | Biso mean: 120.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.656 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -63.2849 Å / Origin y: -67.508 Å / Origin z: 59.4621 Å
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