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Yorodumi- EMDB-12626: Focused refinement of XPD containing part of TFIIH in post-transl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12626 | ||||||||||||||||||
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Title | Focused refinement of XPD containing part of TFIIH in post-translocated state (with ADP-BeF3) | ||||||||||||||||||
Map data | Local resolution filtered and sharpened map | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information 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 holo complex / transcription factor TFIIH core 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 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 / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation 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 / transcription elongation by RNA polymerase I / DNA topological change / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to UV / RNA Polymerase II Pre-transcription Events / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / protein localization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / 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 / DNA helicase / response to oxidative stress / transcription by RNA polymerase II / damaged DNA binding / 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) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||||||||
Authors | Aibara S / Schilbach S / Cramer P | ||||||||||||||||||
Funding support | Germany, 5 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12626.map.gz | 301.3 MB | EMDB map data format | |
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Header (meta data) | emd-12626-v30.xml emd-12626.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12626_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_12626.png | 145.8 KB | ||
Masks | emd_12626_msk_1.map | 347.6 MB | Mask map | |
Others | emd_12626_additional_1.map.gz emd_12626_half_map_1.map.gz emd_12626_half_map_2.map.gz | 204.5 MB 278.4 MB 278.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12626 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12626 | HTTPS FTP |
-Related structure data
Related structure data | 7nvrC 7nvsC 7nvtC 7nvuC 7nvvC 7nvwC 7nvxC 7nvyC 7nvzC 7nw0C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12626.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local resolution filtered and sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_12626_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Local resolution filtered map, unsharpened
File | emd_12626_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_12626_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_12626_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : XPD containing part of TFIIH (with ADP-BeF3)
Entire | Name: XPD containing part of TFIIH (with ADP-BeF3) |
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Components |
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-Supramolecule #1: XPD containing part of TFIIH (with ADP-BeF3)
Supramolecule | Name: XPD containing part of TFIIH (with ADP-BeF3) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 300 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |