8RS8 | pdb_00008rs8

Crystal structure of BRCA1 BRCTs in complex with a RIF1 phosphopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 
    0.179 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.143 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The human RIF1-Long isoform interacts with BRCA1 to promote recombinational fork repair under DNA replication stress.

Dong, Q.Day, M.Saito, Y.Parker, E.Watts, L.P.Kanemaki, M.T.Oliver, A.W.Pearl, L.H.Hiraga, S.I.Donaldson, A.D.

(2025) Nat Commun 16: 5820-5820

  • DOI: https://doi.org/10.1038/s41467-025-60817-y
  • Primary Citation of Related Structures:  
    8RS8

  • PubMed Abstract: 

    RIF1 is a multifunctional protein that regulates DNA replication and repair. RIF1-deficient cells are hypersensitive to DNA replication stress. Of the two alternatively spliced RIF1 isoforms, called RIF1-Short and RIF1-Long, the RIF1-Long isoform is more capable than RIF1-Short in supporting cell recovery from replication stress. Examining replication stress resistance mechanisms specific to RIF1-Long, we find that prolonged replication stress unexpectedly induces interaction of RIF1-Long with BRCA1. Mechanistically, a phosphorylated SPKF motif unique to the RIF1-Long isoform binds the tandem BRCT domain of BRCA1. BRCA1-RIF1-Long interaction is strongly down-regulated through dephosphorylation by RIF1-associated Protein Phosphatase 1. BRCA1-RIF1-Long interaction requires ATR signaling, and occurs predominantly during S phase. Loss of RIF1-Long impairs the formation of RAD51 foci, and reduces the efficiency of homology-mediated repair at broken replication forks. In summary, our investigation establishes RIF1-Long as a new functional binding partner of the BRCA1-BRCT domain, crucial to protect cells from extended DNA replication stress by enabling RAD51-dependent repair of broken replication forks.


  • Organizational Affiliation

    Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Breast cancer type 1 susceptibility protein
A, B, C, D
217Homo sapiensMutation(s): 0 
Gene Names: BRCA1RNF53
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P38398 (Homo sapiens)
Explore P38398 
Go to UniProtKB:  P38398
PHAROS:  P38398
GTEx:  ENSG00000012048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38398
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Telomere-associated protein RIF1
E, F, G, H
11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5UIP0 (Homo sapiens)
Explore Q5UIP0 
Go to UniProtKB:  Q5UIP0
PHAROS:  Q5UIP0
GTEx:  ENSG00000080345 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UIP0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
KA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
LA [auth C],
Y [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth G],
V [auth B],
VA [auth G],
W [auth B],
X [auth B],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
E, F, G, H
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free:  0.179 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.143 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.84α = 90
b = 173.716β = 89.05
c = 74.522γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC302/A24386

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release