9IF9 | pdb_00009if9

Crystal structure of the Pellino 1 FHA domain in complex with a MDC1-TQxF phosphopeptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.211 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

MDC1 mediates Pellino recruitment to sites of DNA double-strand breaks.

Torres Esteban, M.Stewart, M.J.Bragginton, E.Meroni, A.Pellizzari, A.Jeanrenaud, A.Smerdon, S.J.Stucki, M.

(2025) Life Sci Alliance 8

  • DOI: https://doi.org/10.26508/lsa.202403074
  • Primary Citation of Related Structures:  
    9IF9

  • PubMed Abstract: 

    Ubiquitylation is critically implicated in the recognition and repair of DNA double-strand breaks. The adaptor protein MDC1 mediates the recruitment of the key DNA damage responsive E3 ubiquitin ligase RNF8 to the break sites. It does so by directly interacting with RNF8 in a phosphorylation-dependent manner that involves the RNF8 FHA domain, thus initiating targeted chromatin ubiquitylation at the break sites. Here, we report that MDC1 also directly binds to two additional E3 ubiquitin ligases, Pellino 1 and 2, which were recently implicated in the DNA damage response. Through a combination of biochemical, biophysical and X-ray crystallographic approaches, we reveal the molecular details of the MDC1-Pellino complexes. Furthermore, we show that in mammalian cells, MDC1 mediates Pellino recruitment to sites of DNA double-strand breaks by a direct phosphorylation-dependent interaction between the two proteins. Taken together, our findings provide new molecular insights into the ubiquitylation pathways that govern genome stability maintenance.


  • Organizational Affiliation
    • https://ror.org/02crff812 Department of Gynecology, University of Zurich and University Hospital of Zurichhttps://ror.org/01462r250 , Schlieren, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase pellino homolog 1A [auth B],
B [auth A]
251Homo sapiensMutation(s): 0 
Gene Names: PELI1PRISM
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FA3 (Homo sapiens)
Explore Q96FA3 
Go to UniProtKB:  Q96FA3
PHAROS:  Q96FA3
GTEx:  ENSG00000197329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96FA3
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of DNA damage checkpoint protein 1
C, D
11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14676 (Homo sapiens)
Explore Q14676 
Go to UniProtKB:  Q14676
PHAROS:  Q14676
GTEx:  ENSG00000137337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14676
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.211 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.853α = 90
b = 75.087β = 90
c = 165.134γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_163141
Swiss National Science FoundationSwitzerland310030_189141
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T00746X/1
Cancer Research UKUnited KingdomFC001003
Medical Research Council (MRC, United Kingdom)United KingdomFC001003
Wellcome TrustUnited KingdomFC001003

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references