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Yorodumi- PDB-7nvv: XPB-containing part of TFIIH in a post-translocated state (with A... -
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-Basic information
Entry | Database: PDB / ID: 7nvv | ||||||||||||||||||
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Title | XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Initiation | ||||||||||||||||||
Function / homology | Function and homology information core TFIIH complex portion of holo TFIIH complex / nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / transcription factor TFIIE complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex ...core TFIIH complex portion of holo TFIIH complex / nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / transcription factor TFIIE complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / 3'-5' DNA helicase activity / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / transcription factor TFIID complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / ATPase activator activity / RNA Polymerase I Transcription Initiation / DNA topological change / transcription elongation by RNA polymerase I / RNA polymerase II transcribes snRNA genes / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Dual Incision in GG-NER / NoRC negatively regulates rRNA expression / protein localization / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / cellular response to gamma radiation / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / double-stranded DNA binding / response to oxidative stress / DNA helicase / damaged DNA binding / transcription by RNA polymerase II / response to hypoxia / molecular adaptor activity / nuclear speck / positive regulation of apoptotic process / DNA repair / apoptotic process / nucleolus / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) Human mastadenovirus C | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Aibara, S. / Schilbach, S. / Cramer, P. | ||||||||||||||||||
Funding support | Germany, 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 | 7nvv.cif.gz | 228 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvv.ent.gz | 174.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvv ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvv | HTTPS FTP |
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-Related structure data
Related structure data | 12614MC 7nvrC 7nvsC 7nvtC 7nvuC 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
-General transcription ... , 4 types, 4 molecules 257W
#1: Protein | Mass: 52245.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92759 |
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#2: Protein | Mass: 8060.362 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZYL4 |
#3: Protein | Mass: 89404.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19447, DNA helicase |
#6: Protein | Mass: 49516.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083 |
-DNA chain , 2 types, 2 molecules NT
#4: DNA chain | Mass: 32911.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521 |
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#5: DNA chain | Mass: 32508.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521 |
-Protein/peptide , 2 types, 2 molecules YZ
#7: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
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#8: Protein/peptide | Mass: 1379.692 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 3 molecules
#9: Chemical | ChemComp-ADP / |
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#10: Chemical | ChemComp-MG / |
#11: Chemical | ChemComp-BEF / |
-Details
Has ligand of interest | N |
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-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 | Name: XPB-containing part of TFIIH / Type: COMPLEX / Entity ID: #1-#8 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.15 MDa / Experimental value: NO |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 43 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399247 / Symmetry type: POINT |