+Open data
-Basic information
Entry | Database: PDB / ID: 7mka | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of EC+EC (leading EC-focused) | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / pol II | ||||||
Function / homology | Function and homology information nuclear DNA-directed RNA polymerase complex / RNA polymerase complex / RNA polymerase II activity / RNA polymerase II, core complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II ...nuclear DNA-directed RNA polymerase complex / RNA polymerase complex / RNA polymerase II activity / RNA polymerase II, core complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å | ||||||
Authors | Yang, C. / Murakami, K. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Mol Cell / Year: 2022 Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami / Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mka.cif.gz | 772.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mka.ent.gz | 614.7 KB | Display | PDB format |
PDBx/mmJSON format | 7mka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/7mka ftp://data.pdbj.org/pub/pdb/validation_reports/mk/7mka | HTTPS FTP |
---|
-Related structure data
Related structure data | 23888MC 7meiC 7mk9C 7ml0C 7ml1C 7ml2C 7ml3C 7ml4C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-DNA chain , 2 types, 2 molecules NO
#1: DNA chain | Mass: 11967.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
---|---|
#2: DNA chain | Mass: 12338.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
-DNA-directed RNA polymerase ... , 7 types, 7 molecules abcdgik
#3: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: A0A6A5Q1P2, DNA-directed RNA polymerase |
---|---|
#4: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: A0A6A5Q4H2, DNA-directed RNA polymerase |
#5: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z3 |
#6: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTI6 |
#9: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q270 |
#11: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9EWC2 |
#13: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7A1 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules eh
#7: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q456 |
---|---|
#10: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8C2 |
-DNA-directed RNA polymerases II subunit ... , 2 types, 2 molecules jl
#12: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Q6 |
---|---|
#14: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PY05 |
-Protein / RNA chain , 2 types, 2 molecules fr
#15: RNA chain | Mass: 5003.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
---|---|
#8: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZRI7 |
-Non-polymers , 2 types, 10 molecules
#16: Chemical | ChemComp-ZN / #17: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The leading EC of complex EC+EC / Type: COMPLEX Details: bona fide transcription complex, which was generated from in vitro transcription system using isolated proteins from yeast, was achieved via glycerol gradient sedimentation Entity ID: #1-#15 / Source: NATURAL |
---|---|
Molecular weight | Value: 0.5 MDa / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.6 / Details: 20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2565746 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57690 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
|