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- PDB-8rev: Structure of XPD stalled at a Y-fork DNA containing a interstrand... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rev | ||||||
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Title | Structure of XPD stalled at a Y-fork DNA containing a interstrand crosslink | ||||||
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![]() | DNA BINDING PROTEIN / damaged DNA / helicase / XPD / NER / DNA repair / interstrand crosslink | ||||||
Function / homology | ![]() hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA helicase activity / nucleotide-excision repair / DNA helicase / 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 / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA helicase activity / nucleotide-excision repair / DNA helicase / DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Kuper, J. / Hove, T. / Kisker, C. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.5 KB | Display | ![]() |
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PDB format | ![]() | 163.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 19109MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 91847.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 58098.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules EB
#3: DNA chain | Mass: 14448.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#4: DNA chain | Mass: 14329.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#5: Chemical | ChemComp-SF4 / |
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#6: Chemical | ChemComp-ADP / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: XPD-p44 complex bound to DNA / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron 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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237064 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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