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- EMDB-12626: Focused refinement of XPD containing part of TFIIH in post-transl... -

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Basic information

Entry
Database: EMDB / ID: EMD-12626
TitleFocused refinement of XPD containing part of TFIIH in post-translocated state (with ADP-BeF3)
Map data
SampleXPD containing part of TFIIH (with 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsAibara S / Schilbach S / Cramer P
Funding support Germany, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: 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
DepositionMar 16, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 16, 2021-
Current statusJun 16, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12626.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 450 pix.
= 472.5 Å
1.05 Å/pix.
x 450 pix.
= 472.5 Å
1.05 Å/pix.
x 450 pix.
= 472.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 14.0 / Movie #1: 14
Minimum - Maximum-50.83018 - 88.97995
Average (Standard dev.)-0.005186454 (±0.9379945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 472.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z472.500472.500472.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-50.83088.980-0.005

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Supplemental data

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Segmentation: #1

Fileemd_12626_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Local resolution filtered map, unsharpened

Fileemd_12626_additional_1.map
AnnotationLocal resolution filtered map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 1

Fileemd_12626_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 2

Fileemd_12626_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire XPD containing part of TFIIH (with ADP-BeF3)

EntireName: XPD containing part of TFIIH (with ADP-BeF3) / Number of components: 1

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Component #1: protein, XPD containing part of TFIIH (with ADP-BeF3)

ProteinName: XPD containing part of TFIIH (with ADP-BeF3) / Recombinant expression: No
MassTheoretical: 300 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 43 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 399247
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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