+Open data
-Basic information
Entry | Database: PDB / ID: 7nvr | ||||||||||||||||||
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Title | Human Mediator with RNA Polymerase II Pre-initiation complex | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Mediator complex / RNA polymerase II / TFIIH / Pre-initiation complex | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of smooth muscle cell differentiation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / : / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly ...negative regulation of smooth muscle cell differentiation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / : / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / core mediator complex / meiotic sister chromatid cohesion / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / DNA 5'-3' helicase / mediator complex / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / Generic Transcription Pathway / transcription factor TFIIA complex / female germ cell nucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / DNA 3'-5' helicase / [RNA-polymerase]-subunit kinase / limb development / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / cortical actin cytoskeleton / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) Trichoplusia ni (cabbage looper) Human mastadenovirus C | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||||||||
Authors | Rengachari, S. / Schilbach, S. / Aibara, S. / Cramer, P. | ||||||||||||||||||
Funding support | Germany, European Union, 5items
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Citation | Journal: Nature / Year: 2021 Title: Structures of mammalian RNA polymerase II pre-initiation complexes. Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer / Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation. | ||||||||||||||||||
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 | 7nvr.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvr.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 7nvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nvr_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7nvr_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7nvr_validation.xml.gz | 255.9 KB | Display | |
Data in CIF | 7nvr_validation.cif.gz | 423.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvr ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvr | HTTPS FTP |
-Related structure data
Related structure data | 12610MC 7nvsC 7nvtC 7nvuC 7nvvC 7nvwC 7nvxC 7nvyC 7nvzC 7nw0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 8 types, 8 molecules 0389DKLO
+General transcription ... , 9 types, 9 molecules 124567QRW
+DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEFGI
+DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ
+Transcription initiation factor ... , 4 types, 4 molecules MUVX
+DNA chain , 2 types, 2 molecules NT
+Unassigned peptide, likely ... , 2 types, 2 molecules YZ
+Mediator of RNA polymerase II transcription subunit ... , 18 types, 18 molecules abcdefghijklmnopqs
+Unassigned peptide ... , 6 types, 6 molecules rvwxyz
+Non-polymers , 3 types, 20 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 | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
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: 58.56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25967 / Symmetry type: POINT |