[English] 日本語
![](img/lk-miru.gif)
- EMDB-3378: Transcription initiation complex structures elucidate DNA opening... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-3378 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Transcription initiation complex structures elucidate DNA opening (OC3) | |||||||||
![]() | unsharpened OC3 map | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIH-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIH-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / 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 / 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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Plaschka C / Hantsche M / Dienemann C / Burzinski C / Plitzko J / Cramer P | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 94.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.4 KB 14.4 KB | Display Display | ![]() |
Images | ![]() | 140.2 KB | ||
Archive directory | ![]() ![]() | 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 ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unsharpened OC3 map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : yeast Pol II transcription initiation complex (open DNA)
Entire | Name: yeast Pol II transcription initiation complex (open DNA) |
---|---|
Components |
|
-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 |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 45 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 38 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 27 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 91 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 129 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-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 |
---|---|
Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 44 KDa |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.3 mg/mL |
---|---|
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 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
CTF correction | Details: Each particle |
---|---|
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 |