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

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Basic information

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 / pyrimidine dimer repair by nucleotide-excision repair / 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 ...heteroduplex DNA loop binding / nucleotide-excision repair factor 2 complex / pyrimidine dimer repair by nucleotide-excision repair / 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 / Cytosolic iron-sulfur cluster assembly / DNA damage sensor activity / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hair follicle maturation / ventricular system development / response to auditory stimulus / transcription factor TFIIK complex / CAK-ERCC2 complex / bubble DNA binding / embryonic cleavage / UV protection / 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 / DNA 5'-3' helicase / G protein-coupled receptor internalization / adult heart development / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / UV-damage excision repair / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / erythrocyte maturation / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 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 / bone mineralization / 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 / spinal cord development / ATPase activator activity / 3'-5' DNA helicase activity / DNA 3'-5' helicase / DNA topological change / RNA Polymerase I Transcription Initiation / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / hematopoietic stem cell differentiation / embryonic organ development / positive regulation of transcription initiation by RNA polymerase II / protein localization to nucleus / 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 / transcription elongation by RNA polymerase I / response to UV / Cyclin A:Cdk2-associated events at S phase entry / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein kinase holoenzyme complex / Cyclin A/B1/B2 associated events during G2/M transition / transcription by RNA polymerase I / site of DNA damage / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / extracellular matrix organization / hormone-mediated signaling pathway / transcription-coupled nucleotide-excision repair / RNA Polymerase II Pre-transcription Events / insulin-like growth factor receptor signaling pathway / positive regulation of smooth muscle cell proliferation / DNA helicase activity / regulation of autophagy / determination of adult lifespan / post-embryonic development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II
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 / ATP-dependent helicase Rad3/Chl1-like / ERCC3/RAD25/XPB helicase, C-terminal domain / : / 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: To Be Published
Title: Visualisation of stepwise de-repression of TFIIH in global-genome nucleotide excision repair
Authors: de Martin Garrido, N. / Haste, C.A.F. / Feng, J. / Cronin, N.B. / Greber, B.J.
History
DepositionFeb 4, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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 modificationN

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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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