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- EMDB-19109: Structure of XPD stalled at a Y-fork DNA containing a interstrand... -

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Basic information

Entry
Database: EMDB / ID: EMD-19109
TitleStructure of XPD stalled at a Y-fork DNA containing a interstrand crosslink
Map dataFull map of Class1 B-factor sharpened
Sample
  • Complex: XPD-p44 complex bound to DNA
    • Protein or peptide: ATP-dependent DNA helicase CHL1
    • Protein or peptide: General transcription and DNA repair factor IIH
  • DNA: DNA (47-MER)
  • DNA: DNA (46-MER)
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsdamaged DNA / helicase / XPD / NER / DNA repair / interstrand crosslink / DNA BINDING PROTEIN
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA 5'-3' helicase / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / DNA helicase activity / nucleotide-excision repair / DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA 5'-3' helicase / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / DNA helicase activity / nucleotide-excision repair / DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
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 / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase superfamily 1/2, DinG/Rad3-like / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / 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. / Zinc finger C2H2 type domain signature. / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH / DNA 5'-3' helicase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKuper J / Hove T / Kisker C
Funding support Germany, 1 items
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, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19109.png

Downloads & links

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Map

FileDownload / File: emd_19109.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of Class1 B-factor sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.8420988 - 1.8934904
Average (Standard dev.)0.00016427666 (±0.022277405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full Map of Class2 DeepEMhancer sharpened

Fileemd_19109_additional_1.map
AnnotationFull Map of Class2 DeepEMhancer sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class1 Half Map

Fileemd_19109_half_map_1.map
AnnotationClass1 Half Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class 1 Half Map

Fileemd_19109_half_map_2.map
AnnotationClass 1 Half Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : XPD-p44 complex bound to DNA

EntireName: XPD-p44 complex bound to DNA
Components
  • Complex: XPD-p44 complex bound to DNA
    • Protein or peptide: ATP-dependent DNA helicase CHL1
    • Protein or peptide: General transcription and DNA repair factor IIH
  • DNA: DNA (47-MER)
  • DNA: DNA (46-MER)
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: XPD-p44 complex bound to DNA

SupramoleculeName: XPD-p44 complex bound to DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: ATP-dependent DNA helicase CHL1

MacromoleculeName: ATP-dependent DNA helicase CHL1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 91.847172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEFMIDDLPV LFPYPRIYPE QYAYMCDLKK TLDAGGNCVL EMPSGTGKTI TLLSLIVAYQ QHYAEHRKLI YCSRTMSEIE KALVELKAL MKFRAERLGY VEEFRGLGLT SRKNLCLHPS VKREKSGTIV DARCRSLTAG FVKEKKQRGE DVDVCIYHDN L DLLEPHNL ...String:
MEFMIDDLPV LFPYPRIYPE QYAYMCDLKK TLDAGGNCVL EMPSGTGKTI TLLSLIVAYQ QHYAEHRKLI YCSRTMSEIE KALVELKAL MKFRAERLGY VEEFRGLGLT SRKNLCLHPS VKREKSGTIV DARCRSLTAG FVKEKKQRGE DVDVCIYHDN L DLLEPHNL IPNGIWTLDN LLKYGEEHKQ CPYFTARRML QYCNVVIYSY HYLLDPKIAE RVSRDLSSDS IVVFDEAHNI DN VCIEALS TDITEESLRR ATRGAQNLEN RINEMKETDQ QKLQDEYEKL VEGLRGNDDG TREDSFMTSP VLPQDLLKEA VPG NIRRAE HFVAFLRRFI EYLKTRMKVR QVISETPPSF LAHLKEYTFI EKKPLRWCAE RLTSLVRTLE LTNIEDYHAL QEVA TFATL VATYEKGFLL ILEPYESDTA EVPNPVLHFC CLDAAIAIKP VFDKFRNVII TSGTISPLEM YPKMLNFTTV VQESY SMTL ARRSFLPLIV TRGSDQASIS TGFQVRNEPS VVRNYGNLLT EFAKITPDGM VVFFPSYLYM ESIISMWQGM GILDEV WKY KLILVETPDA QETSLALETY RTACCNGRGA VLLCVARGKV SEGIDFDHQY GRTVLCIGVP FQYTESRILK ARLEFLR ET YRIRENDFLS FDAMRHAAQC LGRVLRGKDD YGLMVLADRR FQKKRNQLPK WIAQALLDAD TNLSTDMAVS SARRFLKT M AQPFKAKDQE GISTWSLEDL KRHQQKMDEE RMKELEAQRE KESAPAVERP ADQGRESDYE VDEEEEREMM ALDVGN

UniProtKB: DNA 5'-3' helicase

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Macromolecule #2: General transcription and DNA repair factor IIH

MacromoleculeName: General transcription and DNA repair factor IIH / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 58.098469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADSDGEYVE DLSDDELHDH RPAEAGPHGA RSKAGAGKKR DGKKGKKGSS RHTKAAWEDI QRSWENVVET EDGSITIEAL IEAEKRRRL MRDTTPLQRG IIRHLVLVLD MSFAMAEKDL LPNRYLLTLN YAVDFVREYF EQNPISQMGI IAMRDGIAVR V SDMSGNPA ...String:
MADSDGEYVE DLSDDELHDH RPAEAGPHGA RSKAGAGKKR DGKKGKKGSS RHTKAAWEDI QRSWENVVET EDGSITIEAL IEAEKRRRL MRDTTPLQRG IIRHLVLVLD MSFAMAEKDL LPNRYLLTLN YAVDFVREYF EQNPISQMGI IAMRDGIAVR V SDMSGNPA DHIERLRFWA EHQEPQGNPS LQNALEMCRG ALYHTPSHGT REVLIVYGAL LSSDPGDIHE TISNLVKDRI RV TVVGLAA QVAVCAELCT RTNHGDDSTY AVALHEQHFR ELFLAATIPP PATASSATDK NGANGNANAA STDASLLMMG FPS RTLASA SHVSLCACHS RPSREGYLCT RCRAKVCRLP AECPACGLTL ILSTHLARSY HHLFPLKGWV EVSWAEARKS KQVG CFACL APFPLPPAPG SEKTGKEPTQ KTQGQAQQPP QERQGSSSNS NNAKKTTGIS LATALPEARA VGVSESGRYK CPTCG KHFC IDCDVFAHEV IHNCPGCQAD MRPKQDASSN NIGPANGLNN VVDGDAMVLD

UniProtKB: General transcription and DNA repair factor IIH

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Macromolecule #3: DNA (47-MER)

MacromoleculeName: DNA (47-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.448297 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DA)(DC)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA) (DT)(DT)(DA)(DA)(DG)(DC)(DA)(DT)(DC) (DG)(DC)(DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT) (DG) (DG)(DT)(DC)(DA)(DT)(DA)(DG)

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Macromolecule #4: DNA (46-MER)

MacromoleculeName: DNA (46-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.329309 KDa
SequenceString:
(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC)(DA)(DT) (DG)(DA)(DT)(DT)(DA)(DC)(DG)(DC)(L5R) (DC)(DT)(DG)(DC)(DT)(DT)(DG)(DG)(DA)(DA) (DT)(DC)(DC)(DT)(DG)(DA)(DC)(DG)(DA)(DA) (DC)(DT)(DG)(DT)(DA)(DG)(DA)

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 49.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237064
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

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

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