+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10595 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the RNA Polymerase III-Maf1 complex | |||||||||
Map data | Sharpened and locally filtered EM map | |||||||||
Sample |
| |||||||||
Keywords | Transcription / RNA Polymerase III / Pol III / Maf1 / transcription inhibition | |||||||||
Function / homology | Function and homology information Regulation of PTEN gene transcription / negative regulation of transcription by RNA polymerase III / RNA polymerase III core binding / 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 PTEN gene transcription / negative regulation of transcription by RNA polymerase III / RNA polymerase III core binding / 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 / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase III activity / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / 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 / nucleotidyltransferase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Vorlaender MK / Hagen WJH | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structural basis for RNA polymerase III transcription repression by Maf1. Authors: Matthias K Vorländer / Florence Baudin / Robyn D Moir / René Wetzel / Wim J H Hagen / Ian M Willis / Christoph W Müller / Abstract: Maf1 is a conserved inhibitor of RNA polymerase III (Pol III) that influences phenotypes ranging from metabolic efficiency to lifespan. Here, we present a 3.3-Å-resolution cryo-EM structure of yeast ...Maf1 is a conserved inhibitor of RNA polymerase III (Pol III) that influences phenotypes ranging from metabolic efficiency to lifespan. Here, we present a 3.3-Å-resolution cryo-EM structure of yeast Maf1 bound to Pol III, establishing that Maf1 sequesters Pol III elements involved in transcription initiation and binds the mobile C34 winged helix 2 domain, sealing off the active site. The Maf1 binding site overlaps with that of TFIIIB in the preinitiation complex. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10595.map.gz | 105.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10595-v30.xml emd-10595.xml | 42 KB 42 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10595_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_10595.png | 162.8 KB | ||
Filedesc metadata | emd-10595.cif.gz | 11 KB | ||
Others | emd_10595_half_map_1.map.gz emd_10595_half_map_2.map.gz | 140.3 MB 140.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10595 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10595 | HTTPS FTP |
-Validation report
Summary document | emd_10595_validation.pdf.gz | 752.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_10595_full_validation.pdf.gz | 752 KB | Display | |
Data in XML | emd_10595_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | emd_10595_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10595 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10595 | HTTPS FTP |
-Related structure data
Related structure data | 6tutMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_10595.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened and locally filtered EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: Half map 1, generated by relion refine
File | emd_10595_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1, generated by relion_refine | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2, generated by relion refine
File | emd_10595_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2, generated by relion_refine | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : RNA Polymerase III - Maf1 complex
+Supramolecule #1: RNA Polymerase III - Maf1 complex
+Supramolecule #2: DNA-directed RNA polymerase III
+Supramolecule #3: Repressor of RNA polymerase III transcription MAF1
+Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #18: Repressor of RNA polymerase III transcription MAF1,Repressor of R...
+Macromolecule #19: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 15 mM HEPES, 150 mM (NH4)2SO4, 5 mM DTT |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 6, blot force 2. |
Details | crosslinked with BS3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 10520 / Average exposure time: 14.0 sec. / Average electron dose: 60.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 64 |
---|---|
Output model | PDB-6tut: |