6PE8

Crystal structure of CD40/ABBV-323 FAB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CD40/anti-CD40 antibody complexes which illustrate agonist and antagonist structural switches.

Argiriadi, M.A.Benatuil, L.Dubrovska, I.Egan, D.A.Gao, L.Greischar, A.Hardman, J.Harlan, J.Iyer, R.B.Judge, R.A.Lake, M.Perron, D.C.Sadhukhan, R.Sielaff, B.Sousa, S.Wang, R.McRae, B.L.

(2019) BMC Mol Cell Biol 20: 29-29

  • DOI: https://doi.org/10.1186/s12860-019-0213-4
  • Primary Citation of Related Structures:  
    6PE7, 6PE8, 6PE9

  • PubMed Abstract: 

    CD40 is a 48 kDa type I transmembrane protein that is constitutively expressed on hematopoietic cells such as dendritic cells, macrophages, and B cells. Engagement of CD40 by CD40L expressed on T cells results in the production of proinflammatory cytokines, induces T helper cell function, and promotes macrophage activation. The involvement of CD40 in chronic immune activation has resulted in CD40 being proposed as a therapeutic target for a range of chronic inflammatory diseases. CD40 antagonists are currently being explored for the treatment of autoimmune diseases and several anti-CD40 agonist mAbs have entered clinical development for oncological indications. To better understand the mode of action of anti-CD40 mAbs, we have determined the x-ray crystal structures of the ABBV-323 (anti-CD40 antagonist, ravagalimab) Fab alone, ABBV-323 Fab complexed to human CD40 and FAB516 (anti-CD40 agonist) complexed to human CD40. These three crystals structures 1) identify the conformational CD40 epitope for ABBV-323 recognition 2) illustrate conformational changes which occur in the CDRs of ABBV-323 Fab upon CD40 binding and 3) develop a structural hypothesis for an agonist/antagonist switch in the LCDR1 of this proprietary class of CD40 antibodies. The structure of ABBV-323 Fab demonstrates a unique method for antagonism by stabilizing the proposed functional antiparallel dimer for CD40 receptor via novel contacts to LCDR1, namely residue position R32 which is further supported by a closely related agonist antibody FAB516 which shows only monomeric recognition and no contacts with LCDR1 due to a mutation to L32 on LCDR1. These data provide a structural basis for the full antagonist activity of ABBV-323.


  • Organizational Affiliation

    AbbVie Bioresearch Center, 381 Plantation Street, Worcester, MA, 01605, USA. maria.argiriadi@abbvie.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAB Heavy chainA,
C [auth H]
223Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FAB Light chainB,
D [auth L]
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 5E [auth T],
F [auth U]
173Homo 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: 2.84 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.308α = 90
b = 75.959β = 90
c = 126.093γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description