+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4182 | |||||||||
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Title | RNA Polymerase III closed complex CC1 | |||||||||
Map data | Map sharpened with relion_postprocess | |||||||||
Sample |
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Keywords | Transcription / RNA Polymerase III / TFIIIB / Pre-initiation complex / Closed complex / Brf1 / Bdp1 / TBP / Pol III / Enzyme | |||||||||
Function / homology | Function and homology information RNA polymerase III core binding / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity ...RNA polymerase III core binding / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / regulation of transcription by RNA polymerase III / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / DNA binding, bending / 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 / transcription factor TFIID complex / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase III activity / 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 / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / nucleotidyltransferase activity / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / disordered domain specific binding / ribosome biogenesis / peroxisome / single-stranded DNA binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Vorlaender MK / Khatter H | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2018 Title: Molecular mechanism of promoter opening by RNA polymerase III. Authors: Matthias K Vorländer / Heena Khatter / Rene Wetzel / Wim J H Hagen / Christoph W Müller / Abstract: RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures ...RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site. Our structures reveal an extremely tight, multivalent interaction between TFIIIB and promoter DNA, and explain how TFIIIB recruits Pol III. Together, TFIIIB and Pol III subunit C37 activate the intrinsic transcription factor-like activity of the Pol III-specific heterotrimer to initiate the melting of double-stranded DNA, in a mechanism similar to that of the Pol II system. | |||||||||
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_4182.map.gz | 46.6 MB | EMDB map data format | |
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Header (meta data) | emd-4182-v30.xml emd-4182.xml | 42.2 KB 42.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4182_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_4182.png | 77.6 KB | ||
Masks | emd_4182_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-4182.cif.gz | 11.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4182 | HTTPS FTP |
-Validation report
Summary document | emd_4182_validation.pdf.gz | 359.5 KB | Display | EMDB validaton report |
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Full document | emd_4182_full_validation.pdf.gz | 358.6 KB | Display | |
Data in XML | emd_4182_validation.xml.gz | 11.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4182 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4182 | HTTPS FTP |
-Related structure data
Related structure data | 6f42MC 4180C 4181C 4183C 4184C 6f40C 6f41C 6f44C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10168 (Title: RNA Polymerase III pre-initiation complex / Data size: 4.0 TB / Data #1: Movie frames [micrographs - multiframe] Data #2: Aligned sums of the movie frames without doseweighting [micrographs - single frame] Data #3: Doseweighted aligned sums of the movie frames [micrographs - multiframe] Data #4: Movie frames [micrographs - multiframe] Data #5: Aligned sums of the movie frames without doseweighting [micrographs - single frame] Data #6: Doseweighted aligned sums of the movie frames [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4182.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map sharpened with relion_postprocess | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4182_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA Polymerase III closed complex CC1
+Supramolecule #1: RNA Polymerase III closed complex CC1
+Supramolecule #2: RNA Polymerase
+Supramolecule #3: CC1
+Supramolecule #4: Nucleic acids
+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: TATA-box-binding protein
+Macromolecule #19: Transcription factor IIIB 70 kDa subunit
+Macromolecule #20: Transcription factor TFIIIB component B''
+Macromolecule #21: Non-template DNA
+Macromolecule #22: Template DNA
+Macromolecule #23: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Crosslinked with glutaraldehyde |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.9 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 100 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6f42: |