+Open data
-Basic information
Entry | Database: PDB / ID: 7ml3 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | General transcription factor TFIIH (weak binding) | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | TRANSCRIPTION / PIC / TFIIH / ITC / RNA polymerase II | ||||||||||||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex ...regulation of mitotic recombination / RNA polymerase II promoter clearance / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / DNA duplex unwinding / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 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 / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / ATPase activator activity / Dual incision in TC-NER / DNA helicase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å | ||||||||||||||||||
Authors | Yang, C. / Fujiwara, R. / Kim, H.J. / Gorbea Colon, J.J. / Steimle, S. / Garcia, B.A. / Murakami, K. | ||||||||||||||||||
Funding support | United States, 5items
| ||||||||||||||||||
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
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ml3.cif.gz | 551.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ml3.ent.gz | 423.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ml3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ml3_validation.pdf.gz | 865.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ml3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ml3_validation.xml.gz | 132.9 KB | Display | |
Data in CIF | 7ml3_validation.cif.gz | 191.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7ml3 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7ml3 | HTTPS FTP |
-Related structure data
Related structure data | 23907MC 7meiC 7mk9C 7mkaC 7ml0C 7ml1C 7ml2C 7ml4C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10865 (Title: Structural visualization of de novo initiation of RNA polymerase II transcription Data size: 14.3 TB Data #1: raw micrographs for PIC + ITC maps [micrographs - multiframe] Data #2: raw micrographs for EC+EC map [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 4 types, 4 molecules 3216
#1: Protein | Mass: 38188.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9BTI9 |
---|---|
#2: Protein | Mass: 58602.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2X3 |
#4: Protein | Mass: 58167.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#6: Protein | Mass: 52024.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9FQL5 |
-General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 07
#3: Protein | Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1C1, DNA helicase |
---|---|
#8: Protein | Mass: 95461.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q00578, DNA helicase |
-General transcription and DNA repair factor IIH subunit ... , 2 types, 2 molecules 45
#5: Protein | Mass: 37430.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9C5C2 |
---|---|
#7: Protein | Mass: 8243.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7C1 |
-DNA chain , 2 types, 2 molecules NT
#9: DNA chain | Mass: 9348.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
---|---|
#10: DNA chain | Mass: 9094.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
-Non-polymers , 2 types, 8 molecules
#11: Chemical | ChemComp-ZN / #12: Chemical | ChemComp-SF4 / | |
---|
-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: General transcription factor TFIIH (weak binding) / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101497 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 5OQJ |