5DMI

Structure of the extracellular domain of the CD40 in complex with CHI220 FAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 Biol 428: 2860-2879

  • DOI: 10.1016/j.jmb.2016.05.014
  • Primary Citation of 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 w ...

    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: steven.sheriff@bms.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 5A183Homo sapiensMutation(s): 0 
Gene Names: CD40TNFRSF5
Find proteins for P25942 (Homo sapiens)
Explore P25942 
Go to UniProtKB:  P25942
NIH Common Fund Data Resources
PHAROS  P25942
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chi220 Fab heavy chainH223Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chi220 Fab light chainL213Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.152α = 90
b = 201.152β = 90
c = 63.809γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-09-08 
  • Released Date: 2016-06-01 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • 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