7ZYG

CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

PAXX binding to the NHEJ machinery explains functional redundancy with XLF.

Seif-El-Dahan, M.Kefala-Stavridi, A.Frit, P.Hardwick, S.W.Chirgadze, D.Y.Maia De Oliviera, T.Britton, S.Barboule, N.Bossaert, M.Pandurangan, A.P.Meek, K.Blundell, T.L.Ropars, V.Calsou, P.Charbonnier, J.B.Chaplin, A.K.

(2023) Sci Adv 9: eadg2834-eadg2834

  • DOI: https://doi.org/10.1126/sciadv.adg2834
  • Primary Citation of Related Structures:  
    7ZWA, 7ZYG, 8ASC, 8BH3, 8BHV, 8BHY

  • PubMed Abstract: 

    Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX [paralog of x-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF)] in this mechanism. Here, we report high-resolution cryo-electron microscopy (cryo-EM) and x-ray crystallography structures of the PAXX C-terminal Ku-binding motif bound to Ku70/80 and cryo-EM structures of PAXX bound to two alternate DNA-dependent protein kinase (DNA-PK) end-bridging dimers, mediated by either Ku80 or XLF. We identify residues critical for the Ku70/PAXX interaction in vitro and in cells. We demonstrate that PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK dimers. Last, we show that engagement of both proteins provides a complementary advantage for DNA end synapsis and end joining in cells.


  • Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens)
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Go to UniProtKB:  P12956
PHAROS:  P12956
GTEx:  ENSG00000196419 
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UniProt GroupP12956
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens)
Explore P13010 
Go to UniProtKB:  P13010
PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PAXX204Homo sapiensMutation(s): 0 
Gene Names: PAXXC9orf142XLS
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUH6 (Homo sapiens)
Explore Q9BUH6 
Go to UniProtKB:  Q9BUH6
GTEx:  ENSG00000148362 
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UniProt GroupQ9BUH6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1D [auth F]299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q4 (Homo sapiens)
Explore Q9H9Q4 
Go to UniProtKB:  Q9H9Q4
PHAROS:  Q9H9Q4
GTEx:  ENSG00000187736 
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UniProt GroupQ9H9Q4
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNAE [auth D]15Homo sapiens
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNAF [auth E]15Homo sapiens
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200814/Z/16/Z; 2016

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 2.0: 2023-06-14
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-07-24
    Changes: Data collection, Refinement description