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- EMDB-8816: TFIIH reconstruction from particles sorted for density near the X... -

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Basic information

Database: EMDB / ID: 8816
TitleTFIIH reconstruction from particles sorted for density near the XPD ARCH domain using signal-subtracted classification.
Sampletranscription factor IIH (TFIIH)
SourceHomo sapiens / human / Wikipedia
Map dataHuman TFIIH reconstruction obtained from particle images sorted for density near the XPD ARCH domain using signal-subtracted classification
Methodsingle particle reconstruction, at 5.4 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

DateDeposition: Jul 10, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Oct 4, 2017 / Last update: Feb 14, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0175
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0175
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_8816.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.32 Å
Contour Level:0.0175 (by author), 0.0175 (movie #1):
Minimum - Maximum-0.040265284 - 0.09702903
Average (Standard dev.)2.7291413E-5 (0.0037017267)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0400.0970.000

Supplemental data

Sample components

Entire transcription factor IIH (TFIIH)

EntireName: transcription factor IIH (TFIIH) / Number of components: 1
MassTheoretical: 490 kDa

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

ProteinName: transcription factor IIH (TFIIH) / Recombinant expression: No
MassTheoretical: 490 kDa
SourceSpecies: Homo sapiens / human / Wikipedia / Strain: HeLa
Source (natural)Organelle: Nucleus / Location in cell: Nucleus

Experimental details

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

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
CameraDetector: GATAN K2 (4k x 4k)

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.

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 35900
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 within RELION based on values determined in CTFFIND4.
Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: RELION 3D auto-refinement (gold standard). The final 3D classification used signal-subtracted particle images. The final reconstruction used the corresponding un-subtracted particle images.
Euler angles: Maximum-likelihood 3D refinement within RELION.

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