8BR9

Stapled peptide SP24 in complex with humanised RadA mutant HumRadA22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A recombinant approach for stapled peptide discovery yields inhibitors of the RAD51 recombinase.

Pantelejevs, T.Zuazua-Villar, P.Koczy, O.Counsell, A.J.Walsh, S.J.Robertson, N.S.Spring, D.R.Downs, J.A.Hyvonen, M.

(2023) Chem Sci 14: 13915-13923

  • DOI: https://doi.org/10.1039/d3sc03331g
  • Primary Citation of Related Structures:  
    8BR9, 8C3J, 8C3N

  • PubMed Abstract: 

    Stapling is a macrocyclisation method that connects amino acid side chains of a peptide to improve its pharmacological properties. We describe an approach for stapled peptide preparation and biochemical evaluation that combines recombinant expression of fusion constructs of target peptides and cysteine-reactive divinyl-heteroaryl chemistry as an alternative to solid-phase synthesis. We then employ this workflow to prepare and evaluate BRC-repeat-derived inhibitors of the RAD51 recombinase, showing that a diverse range of secondary structure elements in the BRC repeat can be stapled without compromising binding and function. Using X-ray crystallography, we elucidate the atomic-level features of the staple moieties. We then demonstrate that BRC-repeat-derived stapled peptides can disrupt RAD51 function in cells following ionising radiation treatment.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge CB2 1GA UK teodors.pantelejevs@osi.lv mh256@cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair and recombination protein RadA231Pyrococcus furiosusMutation(s): 27 
Gene Names: radAPF1926
UniProt
Find proteins for O74036 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore O74036 
Go to UniProtKB:  O74036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74036
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Breast cancer type 2 susceptibility protein38Homo sapiensMutation(s): 15 
Gene Names: BRCA2FACDFANCD1
UniProt & NIH Common Fund Data Resources
Find proteins for P51587 (Homo sapiens)
Explore P51587 
Go to UniProtKB:  P51587
GTEx:  ENSG00000139618 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51587
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
RF6
Query on RF6

Download Ideal Coordinates CCD File 
D [auth B]4,6-diethylpyrimidin-2-amine
C8 H13 N3
WWRMBPPGHZDJNZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.464α = 90
b = 38.642β = 90
c = 43.528γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomDTP

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description