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Structure paper

TitlePAXX binding to the NHEJ machinery explains functional redundancy with XLF.
Journal, issue, pagesSci Adv, Vol. 9, Issue 22, Page eadg2834, Year 2023
Publish dateJun 2, 2023
AuthorsMurielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / Madeleine Bossaert / Arun Prasad Pandurangan / Katheryn Meek / Tom L Blundell / Virginie Ropars / Patrick Calsou / Jean-Baptiste Charbonnier / Amanda K Chaplin /
PubMed AbstractNonhomologous 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 ...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.
External linksSci Adv / PubMed:37256950 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.68 - 5.33 Å
Structure data

14995

7zwa

EMDB-14995, PDB-7zwa:
CryoEM structure of Ku heterodimer bound to DNA and PAXX
Method: EM (single particle) / Resolution: 2.8 Å

15022

7zyg

EMDB-15022, PDB-7zyg:
CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF
Method: EM (single particle) / Resolution: 2.68 Å

16044

8bh3

EMDB-16044, PDB-8bh3:
DNA-PK Ku80 mediated dimer bound to PAXX
Method: EM (single particle) / Resolution: 4.55 Å

16070

8bhv

EMDB-16070, PDB-8bhv:
DNA-PK XLF mediated dimer bound to PAXX
Method: EM (single particle) / Resolution: 4.51 Å

16074

8bhy

EMDB-16074, PDB-8bhy:
DNA-PK Ku80 mediated dimer bound to PAXX and XLF
Method: EM (single particle) / Resolution: 5.33 Å

PDB-8asc:
Ku70/80 binds to the Ku-binding motif of PAXX
Method: X-RAY DIFFRACTION / Resolution: 2.95 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
  • human (human)
  • dna molecule (others)
KeywordsDNA BINDING PROTEIN / NHEJ / Ku70 / Ku80 / DNA damage / PAXX / XLF / DNA repair / DNA-PK / DNA-PKcs

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