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- EMDB-3802: The cryo-EM structure of human TFIIH -

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Basic information

Entry
Database: EMDB / ID: 3802
TitleThe cryo-EM structure of human TFIIH
SampleTFIIH
SourceHomo sapiens / human
Map dataPostprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement.
Methodsingle particle reconstruction, at 4.4 Å resolution
AuthorsGreber BJ / Nguyen THD / Fang J / Afonine PV / Adams PD / Nogales E
CitationNature, 2017, 549, 414-417

Nature, 2017, 549, 414-417 Yorodumi Papers
The cryo-electron microscopy structure of human transcription factor IIH.
Basil J Greber / Thi Hoang Duong Nguyen / Jie Fang / Pavel V Afonine / Paul D Adams / Eva Nogales

Validation ReportPDB-ID: 5of4

SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Sep 13, 2017 / Last update: Oct 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5of4
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3802.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.07498146 - 0.12866755
Average (Standard dev.)0.0003252262 (0.0035969224)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
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-0.0750.1290.000

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Supplemental data

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Mask #1

Fileemd_3802_msk_1.map ( map file in CCP4 format, 67109 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsNone
Space group number1

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Mask #1~

Fileemd_3802_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire TFIIH

EntireName: TFIIH / Number of components: 14

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Component #1: protein, TFIIH

ProteinName: TFIIH / Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Component #2: protein, TFIIH core complex

ProteinName: TFIIH core complex / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (natural)Location in cell: Nucleus

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Component #3: protein, TFIIH CDK-activating kinase (CAK) subcomplex

ProteinName: TFIIH CDK-activating kinase (CAK) subcomplex / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (natural)Location in cell: Nucleus

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Component #4: protein, TFIIH basal transcription factor complex helicase XPB su...

ProteinName: TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
Recombinant expression: No
MassTheoretical: 62.426047 kDa
SourceSpecies: Homo sapiens / human

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Component #5: protein, TFIIH basal transcription factor complex helicase XPD subunit

ProteinName: TFIIH basal transcription factor complex helicase XPD subunit
Recombinant expression: No
MassTheoretical: 87.021078 kDa
SourceSpecies: Homo sapiens / human

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Component #6: protein, General transcription factor IIH subunit 4,p52,General t...

ProteinName: General transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
Recombinant expression: No
MassTheoretical: 9.875401 kDa
SourceSpecies: Homo sapiens / human

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Component #7: protein, General transcription factor IIH subunit 2

ProteinName: General transcription factor IIH subunit 2 / Recombinant expression: No
MassTheoretical: 44.481996 kDa
SourceSpecies: Homo sapiens / human

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Component #8: protein, General transcription factor IIH subunit 3

ProteinName: General transcription factor IIH subunit 3 / Recombinant expression: No
MassTheoretical: 34.416008 kDa
SourceSpecies: Homo sapiens / human

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Component #9: protein, General transcription factor IIH subunit 5

ProteinName: General transcription factor IIH subunit 5 / Recombinant expression: No
MassTheoretical: 8.060362 kDa
SourceSpecies: Homo sapiens / human

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Component #10: protein, MAT1

ProteinName: MAT1 / Details: Sequence register unassigned. / Recombinant expression: No
MassTheoretical: 10.571022 kDa
SourceSpecies: Homo sapiens / human

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Component #11: protein, Unassigned secondary structure elements.

ProteinName: Unassigned secondary structure elements. / Details: Sequence unassigned. / Recombinant expression: No
MassTheoretical: 22.996232 kDa
SourceSpecies: Homo sapiens / human

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Component #12: protein, Unassigned secondary structure elements (p52 region)

ProteinName: Unassigned secondary structure elements (p52 region) / Details: Sequence unassigned / Recombinant expression: No
MassTheoretical: 19.762281 kDa
SourceSpecies: Homo sapiens / human

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Component #13: protein, Unassigned secondary structure elements (XPB NTE region)

ProteinName: Unassigned secondary structure elements (XPB NTE region)
Recombinant expression: No
MassTheoretical: 6.656196 kDa
SourceSpecies: Homo sapiens / human

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Component #14: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.0049 mg/ml / pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278.15 K / Humidity: 100 % / Details: 3-4 minute incubation, 2 second blot

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37879 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4500 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 8300 / Sampling size: 5 microns
Details: 8300 micrographs collected in four session with identical acquisition settings. Sessions lasted 4, 2, 4, and 4 days and yielded 1200, 1700, 2800, and 2600 micrographs.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 122900
Details: Micrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected.
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: Correction in RELION based on values determined in CTFFIND4.
Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Details: RELION 3D auto-refinement (gold standard).
Euler angles: Maximum-likelihood 3D refinement within RELION.

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Atomic model buiding

Output model

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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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