5OF4

The cryo-EM structure of human TFIIH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

The cryo-electron microscopy structure of human transcription factor IIH.

Greber, B.J.Nguyen, T.H.D.Fang, J.Afonine, P.V.Adams, P.D.Nogales, E.

(2017) Nature 549: 414-417

  • DOI: https://doi.org/10.1038/nature23903
  • Primary Citation of Related Structures:  
    5OF4

  • PubMed Abstract: 

    Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity.


  • Organizational Affiliation

    California Institute for Quantitative Biology (QB3), University of California, Berkeley, California 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit553Homo sapiensMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
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PHAROS:  P19447
GTEx:  ENSG00000163161 
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UniProt GroupP19447
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunit760Homo sapiensMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
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Find proteins for P18074 (Homo sapiens)
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PHAROS:  P18074
GTEx:  ENSG00000104884 
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UniProt GroupP18074
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4C [auth D]85Homo sapiensMutation(s): 0 
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PHAROS:  Q92759
GTEx:  ENSG00000213780 
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UniProt GroupQ92759
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2D [auth E]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145736 
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UniProt GroupQ13888
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3E [auth F]308Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111358 
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UniProt GroupQ13889
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5F [auth G]71Homo sapiensMutation(s): 0 
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PHAROS:  Q6ZYL4
GTEx:  ENSG00000272047 
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UniProt GroupQ6ZYL4
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
MAT1G [auth H]124Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structure elements.H [auth Z]270Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structure elements (p52 region)I [auth Y]232Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structure elements (XPB NTE region)J [auth X]78Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
K [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIXdevelopment versions
MODEL REFINEMENTREFMAC5.9

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM63072
National Institutes of HealthUnited StatesP01-GM063210

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2017-10-04
    Changes: Database references
  • Version 1.3: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.6: 2024-07-10
    Changes: Data collection