8B4K

Rfa1-N-terminal domain in complex with phosphorylated Ddc2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A.

Yates, L.A.Tannous, E.A.Morgan, R.M.Burgers, P.M.Zhang, X.

(2023) Proc Natl Acad Sci U S A 120: e2300150120-e2300150120

  • DOI: https://doi.org/10.1073/pnas.2300150120
  • Primary Citation of Related Structures:  
    8B4J, 8B4K

  • PubMed Abstract: 

    The cell cycle checkpoint kinase Mec1 ATR and its integral partner Ddc2 ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 "senses" single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage-induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn 2+ . Using electron microscopy and structural modeling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.


  • Organizational Affiliation

    Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor A protein 1
A, B, C
133Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFA1BUF2RPA1YAR007CFUN3
UniProt
Find proteins for P22336 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22336 
Go to UniProtKB:  P22336
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22336
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.506α = 90
b = 34.6β = 90.054
c = 99.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210658/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release