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- EMDB-12614: XPB-containing part of TFIIH in a post-translocated state (with A... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12614 | ||||||||||||||||||
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Title | XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) | ||||||||||||||||||
![]() | Local resolution filtered and sharpened map | ||||||||||||||||||
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![]() | Initiation / TRANSCRIPTION | ||||||||||||||||||
Function / homology | ![]() core TFIIH complex portion of holo TFIIH complex / nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex ...core TFIIH complex portion of holo TFIIH complex / nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / 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 / RNA Polymerase I Transcription Initiation / DNA topological change / ATPase activator activity / RNA polymerase II transcribes snRNA genes / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / isomerase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / 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 / protein localization / double-stranded DNA binding / response to oxidative stress / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / nuclear speck / positive regulation of apoptotic process / DNA repair / nucleolus / apoptotic process / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
![]() | Aibara S / Schilbach S | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 285.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27 KB 27 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 151.1 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() ![]() | 203.4 MB 278.5 MB 278.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nvvMC ![]() 7nvrC ![]() 7nvsC ![]() 7nvtC ![]() 7nvuC ![]() 7nvwC ![]() 7nvxC ![]() 7nvyC ![]() 7nvzC ![]() 7nw0C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Local resolution filtered and sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Local resolution filtered map, unsharpened
File | emd_12614_additional_1.map | ||||||||||||
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Annotation | Local resolution filtered map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1
File | emd_12614_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 2
File | emd_12614_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : XPB-containing part of TFIIH
+Supramolecule #1: XPB-containing part of TFIIH
+Macromolecule #1: General transcription factor IIH subunit 4
+Macromolecule #2: General transcription factor IIH subunit 5
+Macromolecule #3: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #6: General transcription factor IIE subunit 1
+Macromolecule #7: Unassigned peptide, likely XPB
+Macromolecule #8: Unassigned Peptide, likely TFIIE-Beta
+Macromolecule #4: Non-template DNA
+Macromolecule #5: Template DNA
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |