8BHV

DNA-PK XLF mediated dimer bound to PAXX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
DNA-dependent protein kinase catalytic subunitA,
B [auth F]
4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
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Find proteins for P78527 (Homo sapiens)
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GTEx:  ENSG00000253729 
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UniProt GroupP78527
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4C [auth K],
D [auth L],
F [auth N],
G [auth O]
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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Find proteins for Q13426 (Homo sapiens)
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GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4E [auth M],
H [auth P]
911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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Find proteins for P49917 (Homo sapiens)
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GTEx:  ENSG00000174405 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1I [auth Q],
J [auth R]
299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
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GTEx:  ENSG00000187736 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6K [auth a],
N [auth h]
609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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GTEx:  ENSG00000196419 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5L [auth b],
P [auth j]
732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
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Find proteins for P13010 (Homo sapiens)
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GTEx:  ENSG00000079246 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PAXXM [auth c],
O [auth i]
204Homo sapiensMutation(s): 0 
Gene Names: PAXXC9orf142XLS
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GTEx:  ENSG00000148362 
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (26-MER)Q [auth D]27Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (27-MER)R [auth E]28Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (28-MER)S [auth I]24Homo sapiens
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Entity ID: 11
MoleculeChains LengthOrganismImage
DNA (24-MER)T [auth J]24Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

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, Database references, Polymer sequence, Source and taxonomy, Structure summary