|Entry||Database: EMDB / ID: EMD-12625|
|Title||Focused refinement of XPD containing part of TFIIH in pre-translocated state (without ADP-BeF3)|
|Sample||XPD containing part of TFIIH (without ADP-BeF3)|
|Function / homology|
Function and homology information
core TFIIH complex portion of holo TFIIH complex / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription open complex formation at RNA polymerase II promoter / transcription elongation from RNA polymerase I promoter / phosphorylation of RNA polymerase II C-terminal domain / RNA Polymerase I Transcription Termination ...core TFIIH complex portion of holo TFIIH complex / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription open complex formation at RNA polymerase II promoter / transcription elongation from RNA polymerase I promoter / phosphorylation of RNA polymerase II C-terminal domain / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / transcription initiation from RNA polymerase I promoter / HIV Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II HIV Promoter Escape / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation / termination of RNA polymerase I transcription / ATPase activator activity / snRNA transcription by RNA polymerase II / RNA polymerase II general transcription initiation factor activity / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / transcription factor TFIID complex / RNA Polymerase I Transcription Initiation / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II transcribes snRNA genes / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / DNA topological change / RNA Polymerase II Pre-transcription Events / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / embryonic organ development / 7-methylguanosine mRNA capping / response to UV / transcription elongation from RNA polymerase II promoter / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / NoRC negatively regulates rRNA expression / nucleotide-excision repair, DNA duplex unwinding / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / nucleotide-excision repair, DNA incision, 5'-to lesion / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Dual Incision in GG-NER / nucleotide-excision repair, DNA incision / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to gamma radiation / transcription by RNA polymerase II / transcription-coupled nucleotide-excision repair / DNA helicase / double-stranded DNA binding / protein localization / protein N-terminus binding / transcription initiation from RNA polymerase II promoter / response to oxidative stress / protein C-terminus binding / damaged DNA binding / nuclear speck / ATPase / DNA repair / positive regulation of apoptotic process / transcription factor binding / apoptotic process / nucleolus / viral process / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE alpha subunit, C-terminal / Helicase XPB/Ssl2 / Helicase conserved C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / ERCC3/RAD25/XPB C-terminal helicase ...C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE alpha subunit, C-terminal / Helicase XPB/Ssl2 / Helicase conserved C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / ERCC3/RAD25/XPB C-terminal helicase / ERCC3/RAD25/XPB helicase, C-terminal domain / TFIIH subunit TTDA/Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / TFB5-like superfamily / TFIIEalpha/SarR/Rpc3 HTH domain / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription initiation factor IIE / TFIIE alpha subunit / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor E / Zinc finger, TFIIB-type / TFIIB zinc-binding / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase, C-terminal / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIE subunit 1 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.1 Å|
|Authors||Aibara S / Schilbach S / Cramer P|
|Funding support|| Germany, 5 items |
|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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_12625.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.05 Å|
|Symmetry||Space group: 1|
CCP4 map header:
|Projections & Slices|
-Additional map: Local resolution filtered map, unsharpened
|Annotation||Local resolution filtered map, unsharpened|
|Projections & Slices|
-Half map: Unfiltered half map 2
|Annotation||Unfiltered half map 2|
|Projections & Slices|
-Half map: Unfiltered half map 1
-Entire XPD containing part of TFIIH (without ADP-BeF3)
|Entire||Name: XPD containing part of TFIIH (without ADP-BeF3) / Number of components: 1|
-Component #1: protein, XPD containing part of TFIIH (without ADP-BeF3)
|Protein||Name: XPD containing part of TFIIH (without ADP-BeF3) / Recombinant expression: No|
|Mass||Theoretical: 300 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Trichoplusia ni (cabbage looper)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41.1 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
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