+Open data
-Basic information
Entry | Database: PDB / ID: 7ml2 | ||||||||||||||||||
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Title | RNA polymerase II pre-initiation complex (PIC3) | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / PIC / TFIIH / ITC / RNA polymerase II | ||||||||||||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / TFIIH-class transcription factor complex binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / TFIIH-class transcription factor complex binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE 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 / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / 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 / Processing of Capped Intron-Containing Pre-mRNA / 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 / 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 / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / 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 / RNA polymerase III activity / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / acetyltransferase activity / Dual incision in TC-NER / RNA polymerase II activity / positive regulation of translational initiation / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / RNA polymerase I activity / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / 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 / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / nucleic acid binding / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / 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: 3.4 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
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ml2.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ml2.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7ml2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ml2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ml2_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ml2_validation.xml.gz | 261.3 KB | Display | |
Data in CIF | 7ml2_validation.cif.gz | 394.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7ml2 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7ml2 | HTTPS FTP |
-Related structure data
Related structure data | 23906MC 7meiC 7mk9C 7mkaC 7ml0C 7ml1C 7ml3C 7ml4C M: map data used to model this data C: citing same article (ref.) |
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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 |
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1 |
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-Components
+DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCDGIK
+DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules EH
+Protein , 7 types, 7 molecules FMO1423
+DNA-directed RNA polymerases II subunit ... , 2 types, 2 molecules JL
+Transcription initiation factor IIF subunit ... , 2 types, 2 molecules QR
+Transcription initiation factor IIA ... , 2 types, 2 molecules UV
+Transcription initiation factor IIE subunit ... , 2 types, 2 molecules WX
+DNA chain , 2 types, 2 molecules TN
+General transcription and DNA repair factor ... , 4 types, 4 molecules 0657
+Non-polymers , 3 types, 19 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight |
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Source (natural) |
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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 |
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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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69513 Details: Final map is a composite of 3 separately refined domains. Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 5OQJ |