+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3114 | |||||||||
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Title | Structure of an RNA polymerase II pre-initiation complex | |||||||||
Map data | RNA polymerase II pre-initiation complex | |||||||||
Sample |
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Keywords | transcription / pre-initiation complex / RNA polymerase / TFIIE / TFIIH / TFIIB / TBP / TFIIF | |||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA duplex unwinding / 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 / poly(A)+ mRNA export from nucleus / 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 / termination of RNA polymerase II transcription / 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 / RNA polymerase II complex binding / transcription initiation at RNA polymerase III promoter / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / 3'-5' DNA helicase 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / transcription by RNA polymerase III / acetyltransferase activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of RNA polymerase II transcription preinitiation complex assembly / RNA polymerase II activity / positive regulation of transcription initiation by RNA polymerase II / positive regulation of translational initiation / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II, core complex / translesion synthesis / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / transcription antitermination / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | |||||||||
Authors | Murakami K / Tsai K-L / Kalisman N / Bushnell DA / Asturias FJ / Kornberg RD | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structure of an RNA polymerase II preinitiation complex. Authors: Kenji Murakami / Kuang-Lei Tsai / Nir Kalisman / David A Bushnell / Francisco J Asturias / Roger D Kornberg / Abstract: The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the ...The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. | |||||||||
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_3114.map.gz | 12.6 MB | EMDB map data format | |
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Header (meta data) | emd-3114-v30.xml emd-3114.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_3114.png | 195.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3114 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3114 | HTTPS FTP |
-Validation report
Summary document | emd_3114_validation.pdf.gz | 208.8 KB | Display | EMDB validaton report |
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Full document | emd_3114_full_validation.pdf.gz | 207.9 KB | Display | |
Data in XML | emd_3114_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3114 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3114 | HTTPS FTP |
-Related structure data
Related structure data | 5fmfMC 3115C 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_3114.map.gz / Format: CCP4 / Size: 13.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNA polymerase II pre-initiation complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.63 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : yeast RNA polymerase II pre-initiation complex
Entire | Name: yeast RNA polymerase II pre-initiation complex |
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Components |
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-Supramolecule #1000: yeast RNA polymerase II pre-initiation complex
Supramolecule | Name: yeast RNA polymerase II pre-initiation complex / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 1.5 MDa |
-Macromolecule #1: RNA polymerase II pre-initiation complex
Macromolecule | Name: RNA polymerase II pre-initiation complex / type: protein_or_peptide / ID: 1 / Name.synonym: PIC / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast |
Molecular weight | Experimental: 1.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.6 Details: 20 mM HEPES (pH7.6), 5 mM DTT, 2 mM Mg(OAc)2, and 40 mM KOAc |
Grid | Details: 3uL was transferred to Quantifoil and flash frozen in liquid ethane with a Vitrobot. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 14, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2564 / Average electron dose: 40 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: sxcter |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: sparx / Number images used: 7578 |