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- PDB-8rev: Structure of XPD stalled at a Y-fork DNA containing a interstrand... -

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Basic information

Entry
Database: PDB / ID: 8rev
TitleStructure of XPD stalled at a Y-fork DNA containing a interstrand crosslink
Components
  • ATP-dependent DNA helicase CHL1
  • DNA (46-MER)
  • DNA (47-MER)
  • General transcription and DNA repair factor IIH
KeywordsDNA BINDING PROTEIN / damaged DNA / helicase / XPD / NER / DNA repair / interstrand crosslink
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / positive regulation of mitotic recombination / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / four-way junction helicase activity / DNA 5'-3' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / isomerase activity ...single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / positive regulation of mitotic recombination / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / four-way junction helicase activity / DNA 5'-3' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / isomerase activity / nucleotide-excision repair / 4 iron, 4 sulfur cluster binding / damaged DNA binding / transcription by RNA polymerase II / DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / nucleus / metal ion binding
Similarity search - Function
TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like ...TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger C2H2 type domain profile. / von Willebrand factor A-like domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / General transcription and DNA repair factor IIH / DNA 5'-3' helicase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKuper, J. / Hove, T. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: XPD stalled on cross-linked DNA provides insight into damage verification.
Authors: Jochen Kuper / Tamsanqa Hove / Sarah Maidl / Hermann Neitz / Florian Sauer / Maximilian Kempf / Till Schroeder / Elke Greiter / Claudia Höbartner / Caroline Kisker /
Abstract: The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two ...The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.
History
DepositionDec 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase CHL1
D: General transcription and DNA repair factor IIH
E: DNA (47-MER)
B: DNA (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,5026
Polymers178,7234
Non-polymers7792
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8000 Å2
ΔGint-41 kcal/mol
Surface area38540 Å2
MethodPISA

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein ATP-dependent DNA helicase CHL1 / ATP-dependent DNA helicase chl1 / Chromosome loss protein 1 / General transcription and DNA repair ...ATP-dependent DNA helicase chl1 / Chromosome loss protein 1 / General transcription and DNA repair factor IIH helicase subunit XPD


Mass: 91847.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0002930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZH0, DNA helicase
#2: Protein General transcription and DNA repair factor IIH


Mass: 58098.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0002690 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZE6

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DNA chain , 2 types, 2 molecules EB

#3: DNA chain DNA (47-MER)


Mass: 14448.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (46-MER)


Mass: 14329.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 2 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: XPD-p44 complex bound to DNA / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7PHENIXmodel fitting
13PHENIXmodel refinement
14REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237064 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048013
ELECTRON MICROSCOPYf_angle_d0.80710953
ELECTRON MICROSCOPYf_dihedral_angle_d17.6051286
ELECTRON MICROSCOPYf_chiral_restr0.051231
ELECTRON MICROSCOPYf_plane_restr0.0051313

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