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

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Entry
Database: EMDB / ID: 0452
TitleCryo-EM structure of the human TFIIH core complex
Map dataSharpened and low-pass filtered cryo-EM map.
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 / homologyTFIIH subunit TTDA/Tfb5 / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / TFIIH subunit Tfb4/GTF2H3 / Transcription factor TFIIH subunit p52/Tfb2 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Ubiquitin interacting motif / Zinc finger, RING-type / Transcription of the HIV genome / Cdk-activating kinase assembly factor MAT1, centre ...TFIIH subunit TTDA/Tfb5 / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / TFIIH subunit Tfb4/GTF2H3 / Transcription factor TFIIH subunit p52/Tfb2 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Ubiquitin interacting motif / Zinc finger, RING-type / Transcription of the HIV genome / Cdk-activating kinase assembly factor MAT1, centre / Formation of HIV-1 elongation complex containing HIV-1 Tat / Tat-mediated elongation of the HIV-1 transcript / NoRC negatively regulates rRNA expression / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / RNA Polymerase II Pre-transcription Events / Zinc finger, RING/FYVE/PHD-type / Zinc finger, RING-type, conserved site / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Transcription factor Tfb2 (p52) C-terminal domain / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / Ubiquitin-interacting motif (UIM) domain profile. / Zinc finger RING-type profile. / Zinc finger RING-type signature. / Zinc finger, C3HC4 type (RING finger) / TFB5-like superfamily / CDK-activating kinase assembly factor MAT1 / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor Tfb4 / Transcription factor Tfb2 / Transcription factor Tfb2, C-terminal domain / von Willebrand factor A-like domain superfamily / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Formation of TC-NER Pre-Incision Complex / Formation of the HIV-1 Early Elongation Complex / Cyclin D associated events in G1 / RNA Polymerase II Promoter Escape / RNA Polymerase I Chain Elongation / mRNA Capping / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase I Transcription Termination / RNA Polymerase II Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Transcription Elongation / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / TP53 Regulates Transcription of DNA Repair Genes / Gap-filling DNA repair synthesis and ligation in TC-NER / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Dual incision in TC-NER / RNA Polymerase I Transcription Initiation / cyclin-dependent protein kinase activating kinase holoenzyme complex / ventricular system development / negative regulation of DNA helicase activity / core TFIIH complex portion of holo TFIIH complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / transcription elongation from RNA polymerase I promoter / transcription initiation from RNA polymerase I promoter / rDNA binding / termination of RNA polymerase I transcription / RNA polymerase II general transcription initiation factor activity / ATPase activator activity / nucleotide-excision repair, preincision complex stabilization / transcription factor TFIID complex / 7-methylguanosine mRNA capping / transcriptional preinitiation complex / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation from RNA polymerase II promoter / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / nucleotide-excision repair, DNA incision, 5'-to lesion / nucleotide-excision repair / nucleotide-excision repair, DNA incision / rRNA processing / cellular response to gamma radiation / G1/S transition of mitotic cell cycle / transcription-coupled nucleotide-excision repair / response to calcium ion / positive regulation of smooth muscle cell proliferation / protein-containing complex assembly / transcription by RNA polymerase II / double-stranded DNA binding / protein N-terminus binding / transcription initiation from RNA polymerase II promoter / nuclear speck / cell population proliferation / regulation of transcription by RNA polymerase II / DNA repair / nucleolus / protein phosphorylation / negative regulation of apoptotic process
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsGreber BJ / Toso D / Fang J / Nogales E
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
DateDeposition: Jan 10, 2019 / Header (metadata) release: Feb 13, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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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

Fileemd_0452.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.15 Å/pix.
= 294.4 Å
256 pix
1.15 Å/pix.
= 294.4 Å
256 pix
1.15 Å/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 Level:0.0172 (by author), 0.0172 (movie #1):
Minimum - Maximum-0.069341935 - 0.14785278
Average (Standard dev.)0.0001731863 (0.003722968)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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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: 5 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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