8P26

Crystal structure of Arabidopsis thaliana PAXX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Plant PAXX has an XLF-like function and stimulates DNA end joining by the Ku-DNA ligase IV/XRCC4 complex.

Khan, H.Ochi, T.

(2023) Plant J 116: 58-68

  • DOI: https://doi.org/10.1111/tpj.16359
  • Primary Citation of Related Structures:  
    8P26

  • PubMed Abstract: 

    Non-homologous end joining (NHEJ) plays a major role in repairing DNA double-strand breaks and is key to genome stability and editing. The minimal core NHEJ proteins, namely Ku70, Ku80, DNA ligase IV and XRCC4, are conserved, but other factors vary in different eukaryote groups. In plants, the only known NHEJ proteins are the core factors, while the molecular mechanism of plant NHEJ remains unclear. Here, we report a previously unidentified plant ortholog of PAXX, the crystal structure of which showed a similar fold to human 'PAXX'. However, plant PAXX has similar molecular functions to human XLF, by directly interacting with Ku70/80 and XRCC4. This suggests that plant PAXX combines the roles of mammalian PAXX and XLF and that these functions merged into a single protein during evolution. This is consistent with a redundant function of PAXX and XLF in mammals.


  • Organizational Affiliation

    Faculty of Biological Sciences, School of Molecular and Cellular Biology, The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein auxiliary factor-like protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
238Arabidopsis thalianaMutation(s): 0 
Gene Names: MBM17.11MBM17_11At5g64010
UniProt
Find proteins for F4KC77 (Arabidopsis thaliana)
Explore F4KC77 
Go to UniProtKB:  F4KC77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4KC77
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.03α = 90
b = 152.419β = 90
c = 187.087γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-06-28 
  • Deposition Author(s): Ochi, T.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references