+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4147 | |||||||||
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Title | Yeast RNA polymerase I elongation complex at 3.8A | |||||||||
Map data | Sharpened map (B=-149A^2) | |||||||||
Sample |
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Function / homology | Function and homology information 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 / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / regulation of cell size / TP53 Regulates Transcription of DNA Repair Genes ...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 / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / regulation of cell size / 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 / 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 / RNA polymerase III activity / 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 / 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 / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / ribosome biogenesis / peroxisome / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Neyer S / Kunz M / Geiss C / Hantsche M / Hodirnau V-V / Seybert A / Engel C / Scheffer MP / Cramer P / Frangakis AS | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Structure of RNA polymerase I transcribing ribosomal DNA genes. Authors: Simon Neyer / Michael Kunz / Christian Geiss / Merle Hantsche / Victor-Valentin Hodirnau / Anja Seybert / Christoph Engel / Margot P Scheffer / Patrick Cramer / Achilleas S Frangakis / Abstract: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces ...RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4147.map.gz | 43 MB | EMDB map data format | |
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Header (meta data) | emd-4147-v30.xml emd-4147.xml | 36.7 KB 36.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4147_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_4147.png | 66.1 KB | ||
Others | emd_4147_additional.map.gz emd_4147_half_map_1.map.gz emd_4147_half_map_2.map.gz | 35.6 MB 35.9 MB 35.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4147 | HTTPS FTP |
-Validation report
Summary document | emd_4147_validation.pdf.gz | 517.8 KB | Display | EMDB validaton report |
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Full document | emd_4147_full_validation.pdf.gz | 516.9 KB | Display | |
Data in XML | emd_4147_validation.xml.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4147 | HTTPS FTP |
-Related structure data
Related structure data | 5m3fMC 4148C 4149C 5m3mC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4147.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map (B=-149A^2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Filtered to 4.2A
File | emd_4147_additional.map | ||||||||||||
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Annotation | Filtered to 4.2A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1
File | emd_4147_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 2
File | emd_4147_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast RNA polymerase I elongation complex
+Supramolecule #1: Yeast RNA polymerase I elongation complex
+Macromolecule #1: DNA-directed RNA polymerase I subunit RPA190
+Macromolecule #2: DNA-directed RNA polymerase I subunit RPA135
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #7: DNA-directed RNA polymerase I subunit RPA12
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #9: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #14: DNA-directed RNA polymerase I subunit RPA49
+Macromolecule #15: DNA-directed RNA polymerase I subunit RPA34
+Macromolecule #16: DNA-directed RNA polymerase I subunit RPA14
+Macromolecule #17: DNA-directed RNA polymerase I subunit RPA43
+Macromolecule #11: template DNA
+Macromolecule #12: non-template DNA
+Macromolecule #13: RNA
+Macromolecule #18: ZINC ION
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: SULFATE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 13, blotting time 8.5s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |