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- PDB-9pd5: NER dual incision complex - NoF -

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Basic information

Entry
Database: PDB / ID: 9pd5
TitleNER dual incision complex - NoF
Components
  • (General transcription factor IIH subunit ...) x 5
  • DNA
  • DNA Cy5
  • DNA excision repair protein ERCC-5
  • DNA repair protein complementing XP-A cells
  • General transcription and DNA repair factor IIH helicase subunit XPD
  • TFIIH basal transcription factor complex helicase XPB subunit
KeywordsDNA BINDING PROTEIN/DNA / NER / XPA / XPG / XPF / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / 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 / central nervous system myelin formation / base-excision repair, AP site formation / positive regulation of mitotic recombination ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / 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 / central nervous system myelin formation / base-excision repair, AP site formation / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hair follicle maturation / 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 / G protein-coupled receptor internalization / DNA 5'-3' helicase / hydrolase activity, acting on ester bonds / response to UV-C / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / UV-damage excision repair / transcription factor TFIID complex / erythrocyte maturation / RNA polymerase II general transcription initiation factor activity / regulation of mitotic cell cycle phase transition / bone mineralization / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / hematopoietic stem cell proliferation / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / spinal cord development / 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 / 3'-5' DNA helicase activity / DNA topological change / RNA polymerase II complex binding / DNA 3'-5' helicase / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / hematopoietic stem cell differentiation / embryonic organ development / Tat-mediated elongation of the HIV-1 transcript / protein localization to nucleus / response to UV / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / transcription elongation by RNA polymerase I / Formation of RNA Pol II elongation complex / hormone-mediated signaling pathway / transcription by RNA polymerase I / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / RNA Polymerase II Pre-transcription Events / transcription-coupled nucleotide-excision repair / post-embryonic development / determination of adult lifespan / DNA helicase activity / multicellular organism growth / 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 / DNA endonuclease activity / chromosome segregation / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / cellular response to gamma radiation / base-excision repair / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / spindle / enzyme activator activity / 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 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / intracellular protein localization / single-stranded DNA binding / chromosome
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / XPA protein N-terminal / 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 ...XPG/Rad2 endonuclease, eukaryotes / XPA protein N-terminal / 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 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 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 / : / Ubiquitin-binding motif (UBM) domain profile. / 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 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / PIN-like domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / C1-like domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-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 / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
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 / DNA excision repair protein ERCC-5 / General transcription factor IIH subunit 1 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 ...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 / DNA excision repair protein ERCC-5 / General transcription factor IIH subunit 1 / 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: 5.7 Å
AuthorsLi, C.L. / Kim, J. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK075037 United States
CitationJournal: Nature / Year: 2026
Title: Pre-incision structures reveal principles of DNA nucleotide excision repair.
Authors: Eric C L Li / Jinseok Kim / Sem J Brussee / Kaoru Sugasawa / Martijn S Luijsterburg / Wei Yang /
Abstract: Nucleotide excision repair (NER) removes bulky adducts from genomic DNA and prevents the ultraviolet light-sensitivity disease xeroderma pigmentosum, cancer and premature ageing. After initial lesion ...Nucleotide excision repair (NER) removes bulky adducts from genomic DNA and prevents the ultraviolet light-sensitivity disease xeroderma pigmentosum, cancer and premature ageing. After initial lesion recognition by XPC in global genome repair or by stalled RNA polymerases in transcription-coupled repair, a lesion and surrounding DNA duplex are unwound by TFIIH, which includes the ATPases XPB and XPD, and additional NER factors XPA, XPF, XPG and RPA, to form a DNA bubble comprising around 27 nucleotides. The double strand-single strand (ds-ss) junction-specific endonucleases XPF and XPG cleave DNA on the 5' and 3' sides of the lesion, respectively. Here we report the functional steps and atomic structures of the ATPase-driven and lesion-dependent DNA bubble formation and arrangement of the complete NER factors for dual incision. The unwinding of nearly 30 base pairs of DNA depends mainly on the double strand DNA translocase XPB and the duplex dividers XPA and XPF. XPD binds the lesion strand with XPF at the 5' ds-ss junction. XPF cuts the lesion strand only after XPG binds the 3' ds-ss junction. The ERCC1 subunit of XPF facilitates DNA strand separation and recruitment of RPA to the non-lesion strand. These findings provide insights on the causes of human diseases and potential targets for enhancing chemotherapeutic efficacy.
History
DepositionJun 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TFIIH basal transcription factor complex helicase XPB subunit
B: General transcription and DNA repair factor IIH helicase subunit XPD
C: General transcription factor IIH subunit 1
D: General transcription factor IIH subunit 4, p52
E: General transcription factor IIH subunit 2
F: General transcription factor IIH subunit 3
G: General transcription factor IIH subunit 5
K: DNA repair protein complementing XP-A cells
L: DNA Cy5
M: DNA
S: DNA excision repair protein ERCC-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)602,05618
Polymers601,31211
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 , 4 types, 4 molecules ABKS

#1: Protein TFIIH basal transcription factor complex helicase XPB subunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA ...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: 89404.734 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 General transcription and DNA repair factor IIH helicase subunit XPD / TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision ...TFIIH subunit XPD / 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 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 88018.047 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 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: Escherichia coli (E. coli) / References: UniProt: P23025
#11: Protein DNA excision repair protein ERCC-5 / DNA repair protein complementing XP-G cells / XPG / Xeroderma pigmentosum group G-complementing protein


Mass: 133490.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC5, ERCM2, XPG, XPGC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28715, Hydrolases; Acting on ester bonds

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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: 62116.492 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, p52 / 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 / p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 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 chain , 2 types, 2 molecules LM

#9: DNA chain DNA Cy5


Mass: 28476.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain DNA


Mass: 29180.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 7 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#13: 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: NER dual incision complex without XPF / Type: COMPLEX / Entity ID: #1, #3-#10, #2, #11 / Source: RECOMBINANT
Molecular weightValue: 0.88 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMpotassium acetateKOAc1
225 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris1
32 mMcalcium chlorideCaCl21
42 mM(Tris(2-carboxyethyl)phospine)TCEP1
51 %glycerolGlycerol1
60.05 %Octyl glucosideC14H28O61
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13842

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9PHENIX1.21rc1_5127model refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64352 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 8ebt

8ebt


Accession code: 8ebt / Details: C7CAD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 5.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00224337
ELECTRON MICROSCOPYf_angle_d0.42833122
ELECTRON MICROSCOPYf_dihedral_angle_d12.8069219
ELECTRON MICROSCOPYf_chiral_restr0.0373709
ELECTRON MICROSCOPYf_plane_restr0.0034046

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