+Open data
-Basic information
Entry | Database: PDB / ID: 2rf4 | ||||||
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Title | Crystal structure of the RNA Polymerase I subcomplex A14/43 | ||||||
Components | (DNA-directed RNA polymerase I subunit RPA4Polymerase) x 2 | ||||||
Keywords | TRANSFERASE / Transferase DNA/RNA / DNA-binding / Phosphorylation / RNA Polymerase I / Pol I / PolI / RPolI / Nuclear Protein / Nucleolar Protein / Transcription / DDRP / Rpb4/7 / Ribosome biogenesis / DNA-directed RNA polymerase / Nucleus | ||||||
Function / homology | Function and homology information RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / RNA polymerase I complex ...RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / RNA polymerase I complex / ribosome biogenesis / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | ||||||
Authors | Geiger, S.R. / Kuhn, C.D. / Cramer, P. | ||||||
Citation | Journal: Cell / Year: 2007 Title: Functional architecture of RNA polymerase I. Authors: Claus-D Kuhn / Sebastian R Geiger / Sonja Baumli / Marco Gartmann / Jochen Gerber / Stefan Jennebach / Thorsten Mielke / Herbert Tschochner / Roland Beckmann / Patrick Cramer / Abstract: Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron ...Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rf4.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rf4.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 2rf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/2rf4 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/2rf4 | 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24223.096 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA43, RRN12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: P46669, DNA-directed RNA polymerase #2: Protein | Mass: 9675.876 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA43, RRN12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: P50106, DNA-directed RNA polymerase |
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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: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97848 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97848 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. all: 33804 / Num. obs: 33670 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rsym value: 0.077 / Net I/σ(I): 16.14 |
Reflection shell | Resolution: 3.1→3.25 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.97 / Num. unique all: 4457 / Rsym value: 0.399 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.1→30 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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Refine LS restraints |
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