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- EMDB-0452: Cryo-EM structure of the human TFIIH core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0452
TitleCryo-EM structure of the human TFIIH core complex
Map data
SampleTranscription factor IIH (TFIIH)
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription factor IIH subunit ...) x 5
  • CDK-activating kinase assembly factor MAT1
  • (ligand) x 2
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / ventricular system development / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / central nervous system myelin formation / regulation of mitotic recombination / erythrocyte maturation ...cyclin-dependent protein kinase activating kinase holoenzyme complex / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / ventricular system development / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / central nervous system myelin formation / regulation of mitotic recombination / erythrocyte maturation / nucleotide-excision repair factor 3 complex / adult heart development / hair follicle maturation / hair cell differentiation / transcription factor TFIIH core complex / embryonic cleavage / transcription factor TFIIH holo complex / negative regulation of DNA helicase activity / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / UV protection / transcription initiation from RNA polymerase I promoter / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / transcription elongation from RNA polymerase I promoter / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase I transcription / 3'-5' DNA helicase activity / ATPase activator activity / transcription factor TFIID complex / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / bone mineralization / spinal cord development / hematopoietic stem cell differentiation / transcription by RNA polymerase I / 7-methylguanosine mRNA capping / DNA topological change / transcriptional preinitiation complex / regulation of cyclin-dependent protein serine/threonine kinase activity / DNA-dependent ATPase activity / embryonic organ development / regulation of mitotic cell cycle phase transition / transcription elongation from RNA polymerase II promoter / response to UV / DNA helicase / helicase activity / DNA helicase activity / nucleotide-excision repair, DNA duplex unwinding / promoter-specific chromatin binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / chromosome segregation / nucleotide-excision repair / nucleotide-excision repair, DNA incision, 5'-to lesion / protein localization / positive regulation of DNA binding / nucleotide-excision repair, DNA incision / protein-macromolecule adaptor activity / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / positive regulation of smooth muscle cell proliferation / transcription-coupled nucleotide-excision repair / spindle / response to calcium ion / multicellular organism growth / 4 iron, 4 sulfur cluster binding / cell population proliferation / protein-containing complex assembly / double-stranded DNA binding / transcription by RNA polymerase II / extracellular matrix organization / G2/M transition of mitotic cell cycle / protein N-terminus binding / transcription initiation from RNA polymerase II promoter / response to oxidative stress / in utero embryonic development / nucleic acid binding / protein C-terminus binding / response to hypoxia / damaged DNA binding / aging / ATPase activity / nuclear speck / positive regulation of apoptotic process / regulation of transcription by RNA polymerase II / DNA repair / apoptotic process / transcription factor binding / nucleolus / chromatin binding / protein phosphorylation / viral process / negative regulation of apoptotic process / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding
Helicase XPB/Ssl2 / TFIIH subunit Tfb4/GTF2H3 / PH-like domain superfamily / Helical and beta-bridge domain / TFIIH subunit TTDA/Tfb5 / Ssl1-like / Helicase/UvrB, N-terminal / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / BSD domain ...Helicase XPB/Ssl2 / TFIIH subunit Tfb4/GTF2H3 / PH-like domain superfamily / Helical and beta-bridge domain / TFIIH subunit TTDA/Tfb5 / Ssl1-like / Helicase/UvrB, N-terminal / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / BSD domain / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / TFIIH C1-like domain / Cdk-activating kinase assembly factor MAT1/Tfb3 / Ubiquitin interacting motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / von Willebrand factor, type A / RAD3/XPD family / Zinc finger, RING-type / Helicase, C-terminal / TFIIH subunit Ssl1/p44 / DEAD2 / Zinc finger, RING/FYVE/PHD-type / TFB5-like superfamily / ERCC3/RAD25/XPB helicase, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / Helicase XPB/Ssl2, N-terminal domain / TFIIH subunit Tfb1/GTF2H1 / Zinc finger, RING-type, conserved site / Cdk-activating kinase assembly factor MAT1, centre / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase superfamily 1/2, ATP-binding domain / TFIIH p62 subunit, N-terminal / von Willebrand factor A-like domain superfamily / Transcription factor Tfb2, C-terminal domain / Zinc finger C2H2-type
General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGreber BJ / Toso D / Fang J / Nogales E
Funding support United States, Switzerland, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
Swiss National Science FoundationP300PA_160983 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM063210 United States
Swiss National Science FoundationP300PA_174355 Switzerland
CitationJournal: Elife / Year: 2019
Title: The complete structure of the human TFIIH core complex.
Authors: Basil J Greber / Daniel B Toso / Jie Fang / Eva Nogales /
Abstract: Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is ...Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
Validation ReportPDB-ID: 6nmi

SummaryFull reportAbout validation report
History
DepositionJan 10, 2019-
Header (metadata) releaseFeb 13, 2019-
Map releaseMar 13, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nmi
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0452.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å
1.15 Å/pix.
x 256 pix.
= 294.4 Å
1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.0172 / Movie #1: 0.0172
Minimum - Maximum-0.069341935 - 0.14785278
Average (Standard dev.)0.0001731863 (±0.003722968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.400294.400294.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0690.1480.000

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Supplemental data

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Half map: Unfiltered half-map.

Fileemd_0452_half_map_1.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half-map.

Fileemd_0452_half_map_2.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Transcription factor IIH (TFIIH)

EntireName: Transcription factor IIH (TFIIH) / Number of components: 11

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Component #1: protein, Transcription factor IIH (TFIIH)

ProteinName: Transcription factor IIH (TFIIH) / Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPB
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.233492 kDa
SourceSpecies: Human (human)

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Component #3: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPD
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.417766 kDa
SourceSpecies: Human (human)

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Component #4: protein, General transcription factor IIH subunit 1, p62

ProteinName: General transcription factor IIH subunit 1, p62 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.789 kDa
SourceSpecies: Human (human)

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Component #5: protein, General transcription factor IIH subunit 4, p52

ProteinName: General transcription factor IIH subunit 4, p52 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.245156 kDa
SourceSpecies: Human (human)

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Component #6: protein, General transcription factor IIH subunit 2, p44

ProteinName: General transcription factor IIH subunit 2, p44 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.609098 kDa
SourceSpecies: Human (human)

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Component #7: protein, General transcription factor IIH subunit 3, p34

ProteinName: General transcription factor IIH subunit 3, p34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.416008 kDa
SourceSpecies: Human (human)

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Component #8: protein, General transcription factor IIH subunit 5, p8

ProteinName: General transcription factor IIH subunit 5, p8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.060362 kDa
SourceSpecies: Human (human)

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Component #9: protein, CDK-activating kinase assembly factor MAT1

ProteinName: CDK-activating kinase assembly factor MAT1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.873965 kDa
SourceSpecies: Human (human)

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Component #10: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #11: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.0049 mg/mL / pH: 7.9
Support filmGatan Solarus
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Residual beam tilt corrected in RELION 3.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 43478.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 700.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 21437
Details: Images were collected as dose-fractionated movie frames (33 or 50 frames per exposure).

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 138659
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: CTF correction during 3D reconstruction in RELION 3.
Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: Reference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced de novo.
Input PDB model: 5OF4, 4ERN, 5OQJ, 1G25, 5O85, 2DII, 2JNJ
Output model

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