8CN6 | pdb_00008cn6

CD59 in complex with CP-06 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.298 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.234 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8CN6

This is version 1.1 of the entry. See complete history

Literature

Macrocyclic Peptide Probes for Immunomodulatory Protein CD59: Potent Modulators of Bacterial Toxin Activity and Antibody-Dependent Cytotoxicity.

Bickel, J.K.Ahmed, A.I.S.Pidd, A.B.Morgan, R.M.McAllister, T.E.Horrell, S.Couves, E.C.Nagaraj, H.Bartlett, E.J.El Omari, K.Kawamura, A.Bubeck, D.Tate, E.W.

(2025) Angew Chem Int Ed Engl : e202422673-e202422673

  • DOI: https://doi.org/10.1002/anie.202422673
  • Primary Citation Related Structures: 
    8CN6

  • PubMed Abstract: 

    CD59 is an immunomodulatory cell surface receptor associated with human disease. Despite its importance in complement regulation and bacterial pathogenesis, CD59 remains a challenging therapeutic target. Research to date has focused on antibody or protein-based strategies. Here we present a new approach to target CD59 using macrocyclic peptides with low nanomolar affinity for CD59. Through X-ray crystallographic studies and structure-activity relationship (SAR) studies, we identify key interactions that are essential for binding and activity. We find that the macrocyclic peptide CP-06 adopts a beta-hairpin structure and binds CD59 through an intermolecular beta-sheet, mimicking protein-protein interactions of biologically relevant CD59 interaction partners. We create dimeric and lipidated macrocyclic peptide conjugates as enhanced cell-active CD59 inhibitors and show that these probes can be used to modulate both complement-mediated killing of human cells and lytic activity of bacterial virulence factors. Together, our data provide a starting point for future development of macrocyclic peptides to target CD59 activity in diverse cellular contexts.


  • Organizational Affiliation
    • Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK.

Macromolecule Content 

  • Total Structure Weight: 59.11 kDa 
  • Atom Count: 4,063 
  • Modeled Residue Count: 507 
  • Deposited Residue Count: 510 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CD59 glycoprotein
A, B, C, D, E
A, B, C, D, E, F
77Homo sapiensMutation(s): 0 
Gene Names: CD59MIC11MIN1MIN2MIN3MSK21
UniProt & NIH Common Fund Data Resources
Find proteins for P13987 (Homo sapiens)
Explore P13987 
Go to UniProtKB:  P13987
PHAROS:  P13987
GTEx:  ENSG00000085063 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13987
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic peptide CP-06G [auth J],
H [auth G],
I [auth H]
16synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.298 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.94α = 90
b = 85.88β = 90.03
c = 96.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union864751
Cancer Research UKUnited KingdomC24523/A26234
Engineering and Physical Sciences Research CouncilUnited KingdomEP/L015498/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references