8YX1

CD40 in complex with Bleselumab Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab.

Asano, R.Nakakido, M.Perez, J.F.Ise, T.Caaveiro, J.M.M.Nagata, S.Tsumoto, K.

(2024) Biochem Biophys Res Commun 714: 149969-149969

  • DOI: https://doi.org/10.1016/j.bbrc.2024.149969
  • Primary Citation of Related Structures:  
    8YX1, 8YX9

  • PubMed Abstract: 

    CD40 is a member of the tumor necrosis factor receptor superfamily, and it is widely expressed on immune and non-immune cell types. The interaction between CD40 and the CD40 ligand (CD40L) plays an essential function in signaling, and the CD40/CD40L complex works as an immune checkpoint molecule. CD40 has become a therapeutic target, and a variety of agonistic/antagonistic anti-CD40 monoclonal antibodies (mAbs) have been developed. To better understand the mode of action of anti-CD40 mAbs, we determined the X-ray crystal structures of dacetuzumab (agonist) and bleselumab (antagonist) in complex with the extracellular domain of human CD40, respectively. The structure reveals that dacetuzumab binds to CD40 on the top of cysteine-rich domain 1 (CRD1), which is the domain most distant from the cell surface, and it does not compete with CD40L binding. The binding interface of bleselumab spread between CRD2 and CRD1, overlapping with the binding surface of the ligand. Our results offer important insights for future structural and functional studies of CD40 and provide clues to understanding the mechanism of biological response. These data can be applied to developing new strategies for designing antibodies with more therapeutic efficacy.


  • Organizational Affiliation

    Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bleselumab, heavy chainA [auth H],
D [auth A]
229Homo sapiensMutation(s): 0 
Gene Names: Antibody
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bleselumab, light chainB [auth L],
E [auth B]
213Homo sapiensMutation(s): 0 
Gene Names: Antibody
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 5C [auth R],
F [auth C]
179Homo sapiensMutation(s): 0 
Gene Names: CD40TNFRSF5
UniProt & NIH Common Fund Data Resources
Find proteins for P25942 (Homo sapiens)
Explore P25942 
Go to UniProtKB:  P25942
PHAROS:  P25942
GTEx:  ENSG00000101017 
Entity Groups  
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UniProt GroupP25942
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.565α = 90
b = 116.002β = 91.713
c = 121.651γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H05090, 20H03228, 19H05766, 20H02531
Japan Agency for Medical Research and Development (AMED)JapanJP20mk0101170, JP223fa627001, JP223fa727002

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references