+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12615 | ||||||||||||||||||
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Title | TFIIH in a pre-translocated state (without ADP-BeF3) | ||||||||||||||||||
Map data | Local resolution filtered and sharpened map | ||||||||||||||||||
Sample |
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Keywords | Initiation / TRANSCRIPTION | ||||||||||||||||||
Function / homology | Function and homology information 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 / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex ...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 / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / transcription factor TFIIK complex / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / DNA 5'-3' helicase / adult heart development / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / Cyclin E associated events during G1/S transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / regulation of cyclin-dependent protein serine/threonine kinase 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 / spinal cord development / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / Cyclin A/B1/B2 associated events during G2/M transition / bone mineralization / 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 / erythrocyte maturation / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / RNA polymerase II transcribes snRNA genes / intrinsic apoptotic signaling pathway by p53 class mediator / hematopoietic stem cell differentiation / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / hormone-mediated signaling pathway / 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 / DNA helicase activity / positive regulation of smooth muscle cell proliferation / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / isomerase activity / post-embryonic development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chromosome segregation / RNA Polymerase I Promoter Escape / determination of adult lifespan / 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 / response to calcium ion / multicellular organism growth / Cyclin D associated events in G1 / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / G1/S transition of mitotic cell cycle / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / cellular response to gamma radiation / Formation of Incision Complex in GG-NER / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein localization Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Human mastadenovirus C | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||||||||
Authors | Aibara S / Schilbach S | ||||||||||||||||||
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_12615.map.gz | 307.6 MB | EMDB map data format | |
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Header (meta data) | emd-12615-v30.xml emd-12615.xml | 34.1 KB 34.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12615_fsc.xml | 16 KB | Display | FSC data file |
Images | emd_12615.png | 202.2 KB | ||
Masks | emd_12615_msk_1.map | 347.6 MB | Mask map | |
Filedesc metadata | emd-12615.cif.gz | 9.1 KB | ||
Others | emd_12615_additional_1.map.gz emd_12615_half_map_1.map.gz emd_12615_half_map_2.map.gz | 206.2 MB 277.1 MB 276.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12615 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12615 | HTTPS FTP |
-Validation report
Summary document | emd_12615_validation.pdf.gz | 794.1 KB | Display | EMDB validaton report |
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Full document | emd_12615_full_validation.pdf.gz | 793.7 KB | Display | |
Data in XML | emd_12615_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | emd_12615_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12615 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12615 | HTTPS FTP |
-Related structure data
Related structure data | 7nvwMC 7nvrC 7nvsC 7nvtC 7nvuC 7nvvC 7nvxC 7nvyC 7nvzC 7nw0C C: citing same article (ref.) M: atomic model generated by this map |
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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_12615.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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_12615_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally filtered map without sharpening
File | emd_12615_additional_1.map | ||||||||||||
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Annotation | Locally filtered map without sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1
File | emd_12615_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_12615_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TFIIH (without ADP-BeF3)
+Supramolecule #1: TFIIH (without ADP-BeF3)
+Macromolecule #1: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #2: General transcription factor IIH subunit 1
+Macromolecule #3: General transcription factor IIH subunit 4
+Macromolecule #4: CDK-activating kinase assembly factor MAT1
+Macromolecule #5: General transcription factor IIH subunit 3
+Macromolecule #6: General transcription factor IIH subunit 5
+Macromolecule #7: General transcription factor IIH subunit 2
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #11: General transcription factor IIE subunit 1
+Macromolecule #12: Unassigned Peptide, likely XPB
+Macromolecule #13: Unassigned Peptide, likely TFIIE-Beta
+Macromolecule #9: Non-template DNA
+Macromolecule #10: Template DNA
+Macromolecule #14: IRON/SULFUR CLUSTER
+Macromolecule #15: ZINC ION
-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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |