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Yorodumi- EMDB-3378: Transcription initiation complex structures elucidate DNA opening... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3378 | |||||||||
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Title | Transcription initiation complex structures elucidate DNA opening (OC3) | |||||||||
Map data | unsharpened OC3 map | |||||||||
Sample |
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Keywords | Gene expression / Transcription initiation | |||||||||
Function / homology | Function and homology information RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / 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 / 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 / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / 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 / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / disordered domain specific binding / ribosome biogenesis / peroxisome / single-stranded DNA binding / DNA-binding transcription factor binding / transcription regulator complex / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / negative regulation of DNA-templated transcription / chromatin binding / mRNA binding / nucleotide binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.35 Å | |||||||||
Authors | Plaschka C / Hantsche M / Dienemann C / Burzinski C / Plitzko J / Cramer P | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Transcription initiation complex structures elucidate DNA opening. Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer / Abstract: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts. | |||||||||
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_3378.map.gz | 94.2 MB | EMDB map data format | |
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Header (meta data) | emd-3378-v30.xml emd-3378.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_3378.png | 140.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3378 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3378 | HTTPS FTP |
-Validation report
Summary document | emd_3378_validation.pdf.gz | 290.9 KB | Display | EMDB validaton report |
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Full document | emd_3378_full_validation.pdf.gz | 290 KB | Display | |
Data in XML | emd_3378_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3378 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3378 | HTTPS FTP |
-Related structure data
Related structure data | 5fywMC 3375C 3376C 3377C 3379C 3380C 3381C 3382C 3383C 5fz5C 5ip7C 5ip9C 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_3378.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened OC3 map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : yeast Pol II transcription initiation complex (open DNA)
Entire | Name: yeast Pol II transcription initiation complex (open DNA) |
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Components |
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-Supramolecule #1000: yeast Pol II transcription initiation complex (open DNA)
Supramolecule | Name: yeast Pol II transcription initiation complex (open DNA) type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 7 |
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Molecular weight | Theoretical: 890 KDa |
-Macromolecule #1: DNA-directed RNA polymerase II
Macromolecule | Name: DNA-directed RNA polymerase II / type: protein_or_peptide / ID: 1 / Name.synonym: RNA polymerase II / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast |
Molecular weight | Theoretical: 513 KDa |
-Macromolecule #2: Transcription Factor IIA
Macromolecule | Name: Transcription Factor IIA / type: protein_or_peptide / ID: 2 / Name.synonym: TFIIA / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Theoretical: 45 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pOPINE |
-Macromolecule #3: Transcription Factor IIB
Macromolecule | Name: Transcription Factor IIB / type: protein_or_peptide / ID: 3 / Name.synonym: TFIIB / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Theoretical: 38 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pET21b |
-Macromolecule #4: TATA-box-binding protein
Macromolecule | Name: TATA-box-binding protein / type: protein_or_peptide / ID: 4 / Name.synonym: TBP, SPT15 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Theoretical: 27 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pOPINE |
-Macromolecule #5: Transcription Factor IIE
Macromolecule | Name: Transcription Factor IIE / type: protein_or_peptide / ID: 5 / Name.synonym: TFIIE / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Theoretical: 91 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pET21 |
-Macromolecule #6: Transcription Factor IIF
Macromolecule | Name: Transcription Factor IIF / type: protein_or_peptide / ID: 6 / Name.synonym: TFIIF / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Theoretical: 129 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pETDuet-1 |
-Macromolecule #7: synthetic promoter DNA construct (open)
Macromolecule | Name: synthetic promoter DNA construct (open) / type: dna / ID: 7 / Details: Contains a 15 nucleotide mismatch bubble / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 44 KDa |
-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: 7.5 Details: 25 mM HEPES-KOH pH 7.5, 150 mM potassium acetate, 2 mM MgCl2, 5 mM DTT |
Grid | Details: R3.5/1 holey carbon grids (Quantifoil) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: Quantifoil R 3.5/1 holey carbon grids were glow-discharged before deposition of 4.5 microliters of sample. Grids were then blotted for 8.5 s and plunge-frozen in liquid ethane. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Apr 26, 2016 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1756 / Average electron dose: 33 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 11231 |