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The cryo-EM structure of human TFIIH

by single particle reconstruction, at 4.4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.03, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.03, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5of4, Surface level: 0.03, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3802
TitleThe cryo-EM structure of human TFIIH
MapPostprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement.
SampleTFIIH
AuthorsGreber BJ, Nguyen THD
DateDeposition: 2017-07-10, Header release: 2017-08-23, Map release: 2017-09-13, Last update: 2017-09-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.03, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.03, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5of4, Surface level: 0.03, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-5of4

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleNature, Year 2017
TitleThe cryo-electron microscopy structure of human transcription factor IIH
AuthorsGreber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E
LinksDOI: doi:10.1038/nature23903
Map
Fileemd_3802.map.gz ( map file in CCP4 format, 67109 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 A/pix
= 337.92 A
256 pix
1.32 A/pix
= 337.92 A
256 pix
1.32 A/pix
= 337.92 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum: -0.07498146 - 0.12866755
Average (Standard dev.): 0.0003252262 (0.0035969224)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
Unit CellA= B= C: 337.92 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.32 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0750.1290.000
Annotation DetailsPostprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement.
Supplement
Mask Set
Mask: #0
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
DimensionsNumber of Rows: 256 , Number of Columns: 256 , Number of Sections: 256
SpacingSpacing Row: 256 , Spacing Col: 256 , Spacing Sec: 256
OriginOrigin Row: 0 , Origin Col: 0 , Origin Sec: 0
LimitLimit Row: 255 , Limit Col: 255 , Limit Sec: 255
Unit CellA: 337.92 A, B: 337.92 A, C: 337.92 A, alpha: 90 degrees, beta: 90 degrees, gamma: 90 degrees
Axis Order1: X , 2: Y , 3: Z
Statisticsmin.: 0 , max.: 1 , avg.: 0.021517495 , std.: 0.13516468
Pixel SpacingX: 1.32 A, Y: 1.32 A, Z: 1.32 A
Annotation DetailsNone
Space Group Number1
Mask: #1
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Images
Images
Sample
NameTFIIH
Number of Components14
Component #1: protein - TFIIH
Scientific nameTFIIH
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #2: protein - TFIIH core complex
Scientific nameTFIIH core complex
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell Location: Nucleus
Component #3: protein - TFIIH CDK-activating kinase (CAK) subcomplex
Scientific nameTFIIH CDK-activating kinase (CAK) subcomplex
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceCell Location: Nucleus
Component #4: protein - TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
Scientific nameTFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
Theoretical Mass0.062426047 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #5: protein - TFIIH basal transcription factor complex helicase XPD subunit
Scientific nameTFIIH basal transcription factor complex helicase XPD subunit
Theoretical Mass0.087021078 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #6: protein - General transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
Scientific nameGeneral transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
Theoretical Mass0.009875401 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #7: protein - General transcription factor IIH subunit 2
Scientific nameGeneral transcription factor IIH subunit 2
Theoretical Mass0.044481996 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #8: protein - General transcription factor IIH subunit 3
Scientific nameGeneral transcription factor IIH subunit 3
Theoretical Mass0.034416008 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #9: protein - General transcription factor IIH subunit 5
Scientific nameGeneral transcription factor IIH subunit 5
Theoretical Mass0.008060362 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #10: protein - MAT1
Scientific nameMAT1
Theoretical Mass0.010571022 MDa
DetailsSequence register unassigned.
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #11: protein - Unassigned secondary structure elements.
Scientific nameUnassigned secondary structure elements.
Theoretical Mass0.022996232 MDa
DetailsSequence unassigned.
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #12: protein - Unassigned secondary structure elements (p52 region)
Scientific nameUnassigned secondary structure elements (p52 region)
Theoretical Mass0.019762281 MDa
DetailsSequence unassigned
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #13: protein - Unassigned secondary structure elements (XPB NTE region)
Scientific nameUnassigned secondary structure elements (XPB NTE region)
Theoretical Mass0.006656196 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Component #14: ligand - IRON/SULFUR CLUSTER
Scientific nameIRON/SULFUR CLUSTER
Theoretical Mass0.00035164 MDa
Number of Copies1
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.0049 mg/ml
BufferpH: 7.8
Vitrification
Cryogen NameETHANE
Humidity100
Temperature278.15 Kelvin
InstrumentFEI VITROBOT MARK IV
Details3-4 minute incubation, 2 second blot
Imaging
MicroscopeFEI TITAN
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose40 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationCalibrated: 37879
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 4500 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Camera
DetectorGATAN K2 (4k x 4k)
Image Acquisition
#1
Number of Digital Images8300
Sampling Size5
Details8300 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.
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmFOURIER SPACE
SoftwareRELION
CTF CorrectionCorrection in RELION based on values determined in CTFFIND4.
Resolution By Author4.4 A
Resolution MethodFSC 0.143 CUT-OFF
DetailsRELION 3D auto-refinement (gold standard).
Euler Angles DetailsMaximum-likelihood 3D refinement within RELION.
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections122900
DetailsMicrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected.
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-3802-v19.xml (15.3 KB)
emd-3802-v20.xml (36.5 KB)
emd-3802.xml (15.3 KB)
Map dataemd_3802.map.gz (4.6 MB)
Imagesemd_3802.png (140.7 KB)
Masks (Map data of sub-region, etc)emd_3802_msk_1.map (64 MB)
Othersemd_3802_half_map_1.map.gz (49.7 MB)
emd_3802_half_map_2.map.gz (49.7 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3802
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.6 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 26.8 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 6.2 MB
Session file for UCSF-Chimera, 1.9 MB