6TYV

Structure of Ku80 von Willebrand domain complexed with WRN Ku Binding Motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


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Literature

Ligand binding characteristics of the Ku80 von Willebrand domain.

Kim, K.Min, J.Kirby, T.W.Gabel, S.A.Pedersen, L.C.London, R.E.

(2019) DNA Repair (Amst) 85: 102739-102739

  • DOI: 10.1016/j.dnarep.2019.102739
  • Primary Citation of Related Structures:  
    6TYT, 6TYV, 6TYU, 6TYX, 6TYW, 6TYZ

  • PubMed Abstract: 
  • The N-terminal von Willebrand domain of Ku80 supports interactions with a Ku binding motif (KBM) that has been identified in at least three other DNA repair proteins: the non-homologous end joining (NHEJ) scaffold APLF, the modulator of retrovirus infection, MRI, and the Werner syndrome protein (WRN) ...

    The N-terminal von Willebrand domain of Ku80 supports interactions with a Ku binding motif (KBM) that has been identified in at least three other DNA repair proteins: the non-homologous end joining (NHEJ) scaffold APLF, the modulator of retrovirus infection, MRI, and the Werner syndrome protein (WRN). A second, more recently identified Ku binding motif present in XLF and several other proteins (KBMX) has also been reported to interact with this domain. The isolated Ku80 von Willebrand antigen domain (vWA) from Xenopus laevis has a sequence that is 60% identical with the human domain, is readily expressed and has been used to investigate these interactions. Structural characterization of the complexes formed with the KBM motifs in human APLF, MRI, and WRN identify a conserved binding site that is consistent with previously-reported mutational studies. In contrast with the KBM binding site, structural studies indicate that the KBMX site is occluded by a distorted helix. Fluorescence polarization and 19 F NMR studies of a fluorinated XLF C-terminal peptide failed to indicate any interaction with the frog vWA. It was hypothesized that availability of this binding site is conditional, i.e., dependent on specific experimental conditions or other repair factors to make the site available for binding. Modulating the fraction of KBMX-accessible binding site mutationally demonstrated that the more open site is capable of binding the KBMX XLF motif peptide. It is suggested that the conditional nature of KBMX binding limits formation of non-productive complexes so that activation-dependent site availability can more optimally support advancing the synapsis process.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA. Electronic address: london@niehs.nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5A231Xenopus laevisMutation(s): 1 
Gene Names: xrcc5xrcc5-A-provXELAEV_18044412mg
EC: 3.6.4
UniProt
Find proteins for A0A1L8EVE5 (Xenopus laevis)
Explore A0A1L8EVE5 
Go to UniProtKB:  A0A1L8EVE5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THR-THR-ALA-GLN-GLN-ARG-LYS-CYS-PRO-GLU-TRP-MET-ASNB16Homo sapiensMutation(s): 0 
Gene Names: WRNRECQ3RECQL2
EC: 3.6.4.12 (UniProt), 3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14191 (Homo sapiens)
Explore Q14191 
Go to UniProtKB:  Q14191
PHAROS:  Q14191
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.112α = 90
b = 71.351β = 90
c = 79.606γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA-ES102645

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release