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

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Entry
Database: EMDB / ID: 3802
TitleThe cryo-EM structure of human TFIIH
Map dataPostprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement.
SampleTFIIHTranscription factor II H
  • TFIIH core complex
  • TFIIH CDK-activating kinase (CAK) subcomplex
  • (TFIIH basal transcription factor complex helicase ...) x 2
  • (General transcription factor IIH subunit ...) x 4
  • MAT1
  • Unassigned secondary structure elements.
  • (Unassigned secondary structure elements ...) x 2
  • ligand
Function / homologyHelicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / TFIIH subunit Tfb4/GTF2H3 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / TFIIH C1-like domain / VWFA domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Transcription factor TFIIH subunit p52/Tfb2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Formation of RNA Pol II elongation complex ...Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / TFIIH subunit Tfb4/GTF2H3 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / TFIIH C1-like domain / VWFA domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Transcription factor TFIIH subunit p52/Tfb2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Formation of RNA Pol II elongation complex / DEAH-box subfamily ATP-dependent helicases signature. / Formation of the Early Elongation Complex / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the HIV-1 Early Elongation Complex / HIV Transcription Initiation / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / RNA Polymerase II HIV Promoter Escape / P-loop containing nucleoside triphosphate hydrolase / ERCC3/RAD25/XPB C-terminal helicase / Formation of HIV-1 elongation complex containing HIV-1 Tat / Ssl1-like / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / TFB5-like superfamily / Helicase XPB/Ssl2 / von Willebrand factor A-like domain superfamily / Transcription factor Tfb2 / Transcription factor Tfb4 / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / Helicase, C-terminal / Transcription factor TFIIH complex subunit Tfb5 / DEAD_2 / Helical and beta-bridge domain / TFIIH C1-like domain / RAD3/XPD family / Helicase C-terminal domain / von Willebrand factor, type A / Transcription of the HIV genome / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Helicase/UvrB, N-terminal / RNA Polymerase I Transcription Termination / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / ATP-dependent helicase Rad3/Chl1-like / RNA Polymerase I Chain Elongation / Ssl1-like / RNA Polymerase II Transcription Initiation / TFIIH subunit Ssl1/p44 / RNA Polymerase II Transcription Elongation / Zinc finger, RING/FYVE/PHD-type / RNA Polymerase II Transcription Initiation And Promoter Clearance / Zinc finger C2H2-type / RNA Pol II CTD phosphorylation and interaction with CE / Helicase superfamily 1/2, ATP-binding domain / mRNA Capping / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / Cytosolic iron-sulfur cluster assembly / NoRC negatively regulates rRNA expression / TFIIH subunit TTDA/Tfb5 / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Helical and beta-bridge domain / Formation of TC-NER Pre-Incision Complex / RNA Polymerase II Pre-transcription Events / Dual Incision in GG-NER / Tat-mediated elongation of the HIV-1 transcript / DEAD2 / Formation of Incision Complex in GG-NER / TP53 Regulates Transcription of DNA Repair Genes / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / regulation of transposition, RNA-mediated / 5'-3' DNA helicase activity / erythrocyte maturation / regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of mitotic recombination / hair follicle maturation / nucleotide-excision repair factor 3 complex / hair cell differentiation / promoter clearance from RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / embryonic cleavage / DNA translocase activity / 3'-5' DNA helicase activity / transcriptional open complex formation at RNA polymerase II promoter / hematopoietic stem cell differentiation / phosphorylation of RNA polymerase II C-terminal domain / G protein-coupled receptor internalization / ATP-dependent 5'-3' DNA helicase activity / rDNA binding
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsGreber BJ / Nguyen THD / Fang J / Afonine PV / Adams PD / Nogales E
CitationJournal: Nature / Year: 2017
Title: The cryo-electron microscopy structure of human transcription factor IIH.
Authors: 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 17, 2018

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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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5of4
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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
Contrast
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.

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
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 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
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: TFIIHTranscription factor II H / 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)

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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)

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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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.426047 kDa
SourceSpecies: Human (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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.021078 kDa
SourceSpecies: Human (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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.875401 kDa
SourceSpecies: Human (human)

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

ProteinName: General transcription factor IIH subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.481996 kDa
SourceSpecies: Human (human)

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

ProteinName: General transcription factor IIH subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.416008 kDa
SourceSpecies: Human (human)

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

ProteinName: General transcription factor IIH subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.060362 kDa
SourceSpecies: Human (human)

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Component #10: protein, MAT1

ProteinName: MAT1 / Details: Sequence register unassigned. / Number of Copies: 1 / 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. / Number of Copies: 1 / 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 / Number of Copies: 1 / 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)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.656196 kDa
SourceSpecies: Homo sapiens (human)

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Component #14: 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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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37879.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4500.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (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

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: Initial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PHENIX and REFMAC, and fully validated.
Output model

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