5DMJ | pdb_00005dmj

Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 
    0.258 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5DMJ

This is version 1.4 of the entry. See complete history

Literature

Functional Antagonism of Human CD40 Achieved by Targeting a Unique Species-Specific Epitope.

Yamniuk, A.P.Suri, A.Krystek, S.R.Tamura, J.Ramamurthy, V.Kuhn, R.Carroll, K.Fleener, C.Ryseck, R.Cheng, L.An, Y.Drew, P.Grant, S.Suchard, S.J.Nadler, S.G.Bryson, J.W.Sheriff, S.

(2016) J Mol Biology 428: 2860-2879

  • DOI: https://doi.org/10.1016/j.jmb.2016.05.014
  • Primary Citation Related Structures: 
    5DMI, 5DMJ, 5IHL

  • PubMed Abstract: 

    Current clinical anti-CD40 biologic agents include both antagonist molecules for the treatment of autoimmune diseases and agonist molecules for immuno-oncology, yet the relationship between CD40 epitope and these opposing biological outcomes is not well defined. This report describes the identification of potent antagonist domain antibodies (dAbs) that bind to a novel human CD40-specific epitope that is divergent in the CD40 of nonhuman primates. A similarly selected anti-cynomolgus CD40 dAb recognizing the homologous epitope is also a potent antagonist. Mutagenesis, biochemical, and X-ray crystallography studies demonstrate that the epitope is distinct from that of CD40 agonists. Both the human-specific and cynomolgus-specific molecules remain pure antagonists even when formatted as bivalent Fc-fusion proteins, making this an attractive therapeutic format for targeting hCD40 in autoimmune indications.


  • Organizational Affiliation
    • Department of Molecular Discovery Technologies, Bristol-Myers Squibb, Princeton, NJ 08543, USA. Electronic address: aaron.yamniuk@bms.com.

Macromolecule Content 

  • Total Structure Weight: 100.19 kDa 
  • Atom Count: 6,160 
  • Modeled Residue Count: 844 
  • Deposited Residue Count: 912 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 5A,
C [auth D],
E [auth F]
183Homo 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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25942
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
3H65-5 domain antibody (dAb)B,
D [auth E],
F [auth G]
121Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free:  0.258 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.3α = 90
b = 48.7β = 118.2
c = 138.8γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2016-06-01 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary