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- EMDB-0587: Cryo-EM structure of the human TFIIH core complex: Map sorted for... -

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Basic information

Entry
Database: EMDB / ID: 0587
TitleCryo-EM structure of the human TFIIH core complex: Map sorted for the MAT1 RING domain.
Map dataMap sorted for occupancy of the MAT1 RING domain. This map is low-pass filtered to 4.5 Angstroms resolution.
SampleTranscription factor IIH (TFIIH):
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.1 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.
DateDeposition: Feb 19, 2019 / Header (metadata) release: Feb 13, 2019 / Map release: Mar 13, 2019 / Last update: Mar 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0125
  • 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_0587.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:0.0125 (by author), 0.0125 (movie #1):
Minimum - Maximum-0.031204907 - 0.09250763
Average (Standard dev.)0.00019749196 (0.0024125313)
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-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0310.0930.000

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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: 1

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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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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.0049 mg/ml / pH: 7.9
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
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: 81131
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: CTF correction during 3D reconstruction in RELION 3.
Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The map resolution by FSC=0.143 is 4.1 Angstroms. The map was low-pass filtered to 4.5 Angstroms resolution to improve the interpretability of the region of interest.

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: Rigid body docking of the NMR ensemble (PDB ID 1G25) into the region of interest.
Input PDB model: 1G25

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