6TUN

Helicase domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In TFIIH the Arch domain of XPD is mechanistically essential for transcription and DNA repair.

Peissert, S.Sauer, F.Grabarczyk, D.B.Braun, C.Sander, G.Poterszman, A.Egly, J.M.Kuper, J.Kisker, C.

(2020) Nat Commun 11: 1667-1667

  • DOI: https://doi.org/10.1038/s41467-020-15241-9
  • Primary Citation of Related Structures:  
    6TUN

  • PubMed Abstract: 

    The XPD helicase is a central component of the general transcription factor TFIIH which plays major roles in transcription and nucleotide excision repair (NER). Here we present the high-resolution crystal structure of the Arch domain of XPD with its interaction partner MAT1, a central component of the CDK activating kinase complex. The analysis of the interface led to the identification of amino acid residues that are crucial for the MAT1-XPD interaction. More importantly, mutagenesis of the Arch domain revealed that these residues are essential for the regulation of (i) NER activity by either impairing XPD helicase activity or the interaction of XPD with XPG; (ii) the phosphorylation of the RNA polymerase II and RNA synthesis. Our results reveal how MAT1 shields these functionally important residues thereby providing insights into how XPD is regulated by MAT1 and defining the Arch domain as a major mechanistic player within the XPD scaffold.


  • Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPD
A, B
197Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P18074 (Homo sapiens)
Explore P18074 
Go to UniProtKB:  P18074
PHAROS:  P18074
GTEx:  ENSG00000104884 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18074
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1C [auth D],
D [auth C]
77Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
UniProt & NIH Common Fund Data Resources
Find proteins for P51948 (Homo sapiens)
Explore P51948 
Go to UniProtKB:  P51948
PHAROS:  P51948
GTEx:  ENSG00000020426 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51948
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.94α = 90
b = 78.35β = 90
c = 92.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references