skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The complete structure of the human TFIIH core complex

Journal Article · · eLife
DOI:https://doi.org/10.7554/eLife.44771· OSTI ID:1571982

Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1571982
Journal Information:
eLife, Vol. 8; ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 58 works
Citation information provided by
Web of Science

References (126)

Reduced level of the repair/transcription factor TFIIH in trichothiodystrophy journal November 2002
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 journal November 2016
Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH journal September 2015
Prevention of overfitting in cryo-EM structure determination journal July 2012
The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA: IMPLICATIONS FOR EUKARYAL AND ARCHAEAL NUCLEOTIDE EXCISION REPAIR journal February 2010
Conserved XPB Core Structure and Motifs for DNA Unwinding: Implications for Pathway Selection of Transcription or Excision Repair journal April 2006
Nucleotide Excision Repair Driven by the Dissociation of CAK from TFIIH journal July 2008
The relative expression of mutated XPB genes results in xeroderma pigmentosum/Cockayne's syndrome or trichothiodystrophy cellular phenotypes journal June 1999
The Phyre2 web portal for protein modeling, prediction and analysis journal May 2015
Alternative mechanisms of CAK assembly require an assembly factor or an Activating Kinase journal October 1995
Basal Transcription Defect Discriminates between Xeroderma Pigmentosum and Trichothiodystrophy in XPD Patients journal June 2003
Structural basis for DNA duplex separation by a superfamily-2 helicase journal June 2007
p53 and TFIIE  share a common binding site on the Tfb1/p62 subunit of TFIIH journal December 2007
The architecture of the spliceosomal U4/U6.U5 tri-snRNP journal June 2015
Mechanism of DNA loading by the DNA repair helicase XPD journal February 2016
New tools for automated high-resolution cryo-EM structure determination in RELION-3 journal November 2018
SF1 and SF2 helicases: family matters journal June 2010
Xeroderma Pigmentosum-Trichothiodystrophy overlap patient with novel XPD/ERCC2 mutation journal January 2013
Solution Structure of the N-terminal Domain of the Human TFIIH MAT1 Subunit: NEW INSIGHTS INTO THE RING FINGER FAMILY journal October 2000
Real-space refinement in PHENIX for cryo-EM and crystallography journal May 2018
Nucleotide Excision Repair and Transcriptional Regulation: TFIIH and Beyond journal June 2016
p8/TTD-A as a Repair-Specific TFIIH Subunit journal January 2006
Inference of Macromolecular Assemblies from Crystalline State journal September 2007
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Is TFIIH the new Achilles heel of cancer cells? journal August 2017
Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER journal January 2013
Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5' and the 6th phosphodiester bond 3' to the photodimer. journal April 1992
Gctf: Real-time CTF determination and correction journal January 2016
Enzymatic Activities and DNA Substrate Specificity of Mycobacterium tuberculosis DNA Helicase XPB journal May 2012
Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate journal June 2017
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution journal March 2012
Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy journal October 2003
A Yeast Four-hybrid System Identifies Cdk-activating Kinase as a Regulator of the XPD Helicase, a Subunit of Transcription Factor IIH journal July 2001
Structure of the Tfb1/p53 Complex: Insights into the Interaction between the p62/Tfb1 Subunit of TFIIH and the Activation Domain of p53 journal June 2006
Structures of transcription pre-initiation complex with TFIIH and Mediator journal November 2017
Domain Architecture of the p62 Subunit from the Human Transcription/Repair Factor TFIIH Deduced by Limited Proteolysis and Mass Spectrometry Analysis journal November 2004
Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA journal October 2000
A novel cyclin associates with M015/CDK7 to form the CDK-activating kinase journal August 1994
The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH journal August 2017
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
Transcription without XPB Establishes a Unified Helicase-Independent Mechanism of Promoter Opening in Eukaryotic Gene Expression journal February 2017
A structure-specific nucleic acid-binding domain conserved among DNA repair proteins journal May 2014
Mutations in the XPD helicase gene result in XP and TTD phenotypes, preventing interaction between XPD and the p44 subunit of TFIIH journal October 1998
The cryo-electron microscopy structure of human transcription factor IIH journal September 2017
Semi-automated selection of cryo-EM particles in RELION-1.3 journal February 2015
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Crystal Structure of the Rad3/XPD Regulatory Domain of Ssl1/p44 journal February 2015
Structure of an RNA polymerase II preinitiation complex journal October 2015
A eukaryotic SPB/ERCC3-like helicase in Mycobacterium leprae? journal November 1997
Reconstitution of the Transcription Factor TFIIH journal January 1999
Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION journal June 2018
Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways journal October 2017
Focus: The interface between data collection and data processing in cryo-EM journal May 2017
Two-Step Recognition of DNA Damage for Mammalian Nucleotide Excision Repair: Directional Binding of the XPC Complex and DNA Strand Scanning journal November 2009
Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution journal February 2016
Distinct Regions of MAT1 Regulate cdk7 Kinase and TFIIH Transcription Activities journal May 2000
ARCH domain of XPD, an anchoring platform for CAK that conditions TFIIH DNA repair and transcription activities journal February 2013
Structural basis of transcription initiation by RNA polymerase II journal February 2015
Sampling the conformational space of the catalytic subunit of human γ-secretase journal December 2015
Transcription-Associated Breaks in Xeroderma Pigmentosum Group D Cells from Patients with Combined Features of Xeroderma Pigmentosum and Cockayne Syndrome journal August 2005
Cdk-activating kinase complex is a component of human transcription factor TFIIH journal March 1995
Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex journal September 2016
Mediator structure and rearrangements required for holoenzyme formation journal March 2017
Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation journal March 2015
Crystal Structure of a Heat-inducible Transcriptional Repressor HrcA from Thermotoga maritima: Structural Insight into DNA Binding and Dimerization journal July 2005
Structural and Functional Characterization of the Human DNA Repair Helicase XPD by Comparative Molecular Modeling and Site-directed Mutagenesis of the Bacterial Repair Protein UvrB journal November 2002
A temperature-sensitive disorder in basal transcription and DNA repair in humans journal March 2001
Subunit architecture of general transcription factor TFIIH journal January 2012
p44/SSL1, the Regulatory Subunit of the XPD/RAD3 Helicase, Plays a Crucial Role in the Transcriptional Activity of TFIIH journal August 2000
Near-atomic resolution visualization of human transcription promoter opening journal May 2016
Structural basis for group A trichothiodystrophy journal August 2008
Polymorphisms in the human XPD (ERCC2) gene, DNA repair capacity and cancer susceptibility: An appraisal journal September 2005
XPA: A key scaffold for human nucleotide excision repair journal August 2016
Inhibition of Rad3 DNA helicase activity by DNA adducts and abasic sites: implications for the role of a DNA helicase in damage-specific incision of DNA journal January 1993
A unified model for the molecular basis of Xeroderma pigmentosum -Cockayne Syndrome journal January 2015
Different forms of TFIIH for transcription and DNA repair: Holo-TFIIH and a nucleotide excision repairosome journal January 1995
A summary of mutations in the UV-sensitive disorders: Xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy journal January 1999
Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH journal April 1997
Distinct Roles for the XPB/p52 and XPD/p44 Subcomplexes of TFIIH in Damaged DNA Opening during Nucleotide Excision Repair journal April 2007
DNA translocation mechanism of an XPD family helicase journal December 2018
Improved methods for building protein models in electron density maps and the location of errors in these models journal March 1991
TFIIH contains a PH domain involved in DNA nucleotide excision repair journal June 2004
Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening journal July 2012
Structural visualization of key steps in human transcription initiation journal February 2013
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy journal February 2017
The rem Mutations in the ATP-Binding Groove of the Rad3/XPD Helicase Lead to Xeroderma pigmentosum-Cockayne Syndrome-Like Phenotypes journal December 2014
Crystal Structure of the FeS Cluster–Containing Nucleotide Excision Repair Helicase XPD journal June 2008
DNA Repair and Transcriptional Deficiencies Caused by Mutations in the Drosophila p52 Subunit of TFIIH Generate Developmental Defects and Chromosome Fragility journal March 2007
p52 Mediates XPB Function within the Transcription/Repair Factor TFIIH journal June 2002
Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation: Crystal structure of an XPD-DNA complex journal November 2011
XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations journal May 2008
Mechanism of open complex and dual incision formation by human nucleotide excision repair factors journal November 1997
A Postincision-Deficient TFIIH Causes Replication Fork Breakage and Uncovers Alternative Rad51- or Pol32-Mediated Restart Mechanisms journal March 2010
In TFIIH, XPD Helicase Is Exclusively Devoted to DNA Repair journal September 2014
Deciphering key features in protein structures with the new ENDscript server journal April 2014
DNA repair gene RAD3 of S. cerevisiae is essential for transcription by RNA polymerase II journal January 1994
Features and development of Coot journal March 2010
RELION: Implementation of a Bayesian approach to cryo-EM structure determination journal December 2012
Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH journal July 2016
Sequential and ordered assembly of a large DNA repair complex on undamaged chromatin journal August 2014
DNA Quality Control by a Lesion Sensor Pocket of the Xeroderma Pigmentosum Group D Helicase Subunit of TFIIH journal February 2013
Expanding the boundaries of cryo-EM with phase plates journal October 2017
TFIIH with Inactive XPD Helicase Functions in Transcription Initiation but Is Defective in DNA Repair journal February 2000
Regulation of endonuclease activity in human nucleotide excision repair journal July 2011
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega journal January 2011
MAT1 (‘menage à trois’) a new RING finger protein subunit stabilizing cyclin H-cdk7 complexes in starfish and Xenopus CAK. journal October 1995
Structure of the DNA Repair Helicase XPD journal May 2008
Strand-specific Recognition of DNA Damages by XPD Provides Insights into Nucleotide Excision Repair Substrate Versatility journal December 2013
Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE journal January 2013
Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition journal July 2016
Human cyclin-dependent kinase-activating kinase exists in three distinct complexes. journal June 1996
A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A journal June 2004
The DNA Repair Helicases XPD and FancJ Have Essential Iron-Sulfur Domains journal September 2006
Molecular insights into the recruitment of TFIIH to sites of DNA damage journal August 2009
Solution Structure and Self-association Properties of the p8 TFIIH Subunit Responsible for Trichothiodystrophy journal April 2007
Tripartite DNA Lesion Recognition and Verification by XPC, TFIIH, and XPA in Nucleotide Excision Repair journal September 2015
Predictive Value of Single Nucleotide Polymorphisms of ERCC1, XPA, XPC, XPD and XPG Genes, Involved in NER Mechanism in Patients with Advanced NSCLC Treated with Cisplatin and Gemcitabine journal July 2018
A Role of the C-terminal Part of p44 in the Promoter Escape Activity of Transcription Factor IIH journal April 2001
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen journal August 2020
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation journal February 2021
Structures of mammalian RNA polymerase II pre-initiation complexes journal April 2021
Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder journal April 2021
DNA quality control by a lesion sensor pocket of the xeroderma pigmentosum group D helicase subunit of TFIIH text January 2013
Near-atomic resolution visualization of human transcription promoter opening journal May 2017
Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5' and the 6th phosphodiester bond 3' to the photodimer. text January 1992
PHENIX: a comprehensive Python-based system for macromolecular structure solution. text January 2010

Cited By (7)

The pore structure of Clostridium perfringens epsilon toxin journal June 2019
Transcription preinitiation complex structure and dynamics provide insight into genetic diseases journal May 2019
Nucleotide excision repair genes shaping embryonic development journal October 2019
Gene modification by fast‐track recombineering for cellular localization and isolation of components of plant protein complexes journal July 2019
Drosophila as a Model Organism to Understand the Effects during Development of TFIIH-Related Human Diseases journal January 2020
The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair journal November 2020
Structural basis of TFIIH activation for nucleotide excision repair journal June 2019