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- PDB-28ke: Cryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound t... -

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Entry
Database: PDB / ID: 28ke
TitleCryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound to bulky lesion-mimic DNA
Components
  • (DNA repair protein complementing XP- ...) x 2
  • (General transcription factor IIH subunit ...) x 5
  • CDK-activating kinase assembly factor MAT1
  • DNA lesion strand
  • DNA non-lesion strand
  • General transcription and DNA repair factor IIH helicase subunit XPB
  • TFIIH basal transcription factor complex helicase XPD subunit
KeywordsDNA BINDING PROTEIN / Nucleotide excision repair / DNA Repair / helicase / transcription factor
Function / homology
Function and homology information


heteroduplex DNA loop binding / nucleotide-excision repair factor 2 complex / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / DNA damage sensor activity ...heteroduplex DNA loop binding / nucleotide-excision repair factor 2 complex / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / DNA damage sensor activity / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / hair cell differentiation / response to auditory stimulus / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription factor TFIIK complex / CAK-ERCC2 complex / bubble DNA binding / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / G protein-coupled receptor internalization / DNA 5'-3' helicase / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / embryonic organ development / UV-damage excision repair / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / ATPase activator activity / DNA topological change / RNA Polymerase I Transcription Initiation / response to UV / DNA 3'-5' helicase / protein localization to nucleus / 3'-5' DNA helicase activity / Tat-mediated elongation of the HIV-1 transcript / Cyclin E associated events during G1/S transition / Formation of HIV-1 elongation complex containing HIV-1 Tat / mismatch repair / SUMOylation of DNA damage response and repair proteins / Cyclin A:Cdk2-associated events at S phase entry / Formation of HIV elongation complex in the absence of HIV Tat / hormone-mediated signaling pathway / Cyclin A/B1/B2 associated events during G2/M transition / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / regulation of G1/S transition of mitotic cell cycle / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / positive regulation of smooth muscle cell proliferation / transcription-coupled nucleotide-excision repair / DNA helicase activity / site of DNA damage / TP53 Regulates Transcription of DNA Repair Genes / G1/S transition of mitotic cell cycle / chromosome segregation / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription elongation by RNA polymerase II / base-excision repair / NoRC negatively regulates rRNA expression / transcription by RNA polymerase II / DNA Damage Recognition in GG-NER / spindle / intracellular protein localization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / sequence-specific double-stranded DNA binding / Cyclin D associated events in G1 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to oxidative stress / double-stranded DNA binding / 5'-3' DNA helicase activity / damaged DNA binding
Similarity search - Function
XPA protein N-terminal / Rad4 beta-hairpin domain 2 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily ...XPA protein N-terminal / Rad4 beta-hairpin domain 2 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Transglutaminase-like superfamily / : / MAT1 C-terminal CAK anchor / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ERCC3/RAD25/XPB helicase, C-terminal domain / : / ATP-dependent helicase Rad3/Chl1-like / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Putative DNA-binding domain superfamily / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / C1-like domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / PH-like domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / DNA repair protein complementing XP-C cells / General transcription factor IIH subunit 2 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / DNA repair protein complementing XP-C cells / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
Authorsde Martin Garrido, N. / Haste, C.A.F. / Feng, J. / Cronin, N.B. / Greber, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair.
Authors: Natàlia de Martín Garrido / Callum A F Haste / Junjie Feng / Nora B Cronin / Basil J Greber /
Abstract: Nucleotide excision repair (NER) is a crucial DNA repair pathway that is orchestrated by transcription factor IIH (TFIIH) in eukaryotic cells. TFIIH is a multifunctional complex that contains two DNA ...Nucleotide excision repair (NER) is a crucial DNA repair pathway that is orchestrated by transcription factor IIH (TFIIH) in eukaryotic cells. TFIIH is a multifunctional complex that contains two DNA helicase/DNA translocase subunits and a kinase module, different subsets of which act in NER, transcription initiation, and cell cycle control. To ensure fidelity despite multifunctionality, the DNA helicase activity of TFIIH is autoinhibited in its free form or when the factor engages in transcription initiation. While the release of the kinase module has been identified as a key step in TFIIH activation, the molecular mechanisms controlling this step and concomitant structural changes in TFIIH are incompletely understood. Here, we determine high-resolution structures of three NER intermediates that visualize how TFIIH arrives at sites of DNA damage in an autoinhibited state and how autoinhibition is released via previously undescribed intermediates. These findings contribute to a mechanistic understanding of human DNA repair.
History
DepositionFeb 4, 2026Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription and DNA repair factor IIH helicase subunit XPB
B: TFIIH basal transcription factor complex helicase XPD subunit
C: General transcription factor IIH subunit 1
D: General transcription factor IIH subunit 4
E: General transcription factor IIH subunit 2
F: General transcription factor IIH subunit 3
G: General transcription factor IIH subunit 5
H: CDK-activating kinase assembly factor MAT1
I: DNA repair protein complementing XP-C cells
N: DNA repair protein complementing XP-A cells
L: DNA lesion strand
M: DNA non-lesion strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)595,86919
Polymers595,12512
Non-polymers7447
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules ABH

#1: Protein General transcription and DNA repair factor IIH helicase subunit XPB / TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair ...TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 91300.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19447, DNA helicase
#2: Protein TFIIH basal transcription factor complex helicase XPD subunit / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 ...Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 88306.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18074, DNA helicase
#8: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 35873.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51948

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General transcription factor IIH subunit ... , 5 types, 5 molecules CDEFG

#3: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 66403.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32780
#4: Protein General transcription factor IIH subunit 4 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92759
#5: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44481.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13888
#6: Protein General transcription factor IIH subunit 3 / Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH ...Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH polypeptide 3 / TFIIH basal transcription factor complex p34 subunit


Mass: 34416.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13889
#7: Protein General transcription factor IIH subunit 5 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6ZYL4

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DNA repair protein complementing XP- ... , 2 types, 2 molecules IN

#9: Protein DNA repair protein complementing XP-C cells / Xeroderma pigmentosum group C-complementing protein / p125


Mass: 106142.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPC, XPCC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01831
#10: Protein DNA repair protein complementing XP-A cells / Xeroderma pigmentosum group A-complementing protein


Mass: 31422.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P23025

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DNA chain , 2 types, 2 molecules LM

#11: DNA chain DNA lesion strand


Mass: 14534.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain DNA non-lesion strand


Mass: 21938.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 7 molecules

#13: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT
Molecular weightValue: 0.72682 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHepesHEPES-KOH1
2150 mMPotassium chlorideKCl1
30.5 mMTris(2-carboxyethyl)phosphine hydrochlorideTCEP1
42 mMMagnesium chlorideMgCl21
53 % (w/v)TrehaloseTrehalose1
60.01 % (v/v)NP-40NP-401
SpecimenConc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293.15 K / Details: Leica EM GP2

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2Topazparticle selection
3EPUimage acquisition
5cryoSPARC4.6.2CTF correction
10PHENIX1.21.1_5286model refinement
11cryoSPARC4.6.2initial Euler assignment
12RELION5.0.0final Euler assignment
13RELION5.0.0classification
14RELION5.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2486323 / Details: Particles selected after 2D classification
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43458 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324683
ELECTRON MICROSCOPYf_angle_d0.5633525
ELECTRON MICROSCOPYf_dihedral_angle_d12.833606
ELECTRON MICROSCOPYf_chiral_restr0.0413753
ELECTRON MICROSCOPYf_plane_restr0.0044138

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