5IHL

STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.268 

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:  

  • 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: aaron.yamniuk@bms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 5
A, D, F, H
183Homo sapiensMutation(s): 0 
Gene Names: CD40 (TNFRSF5)
Find proteins for P25942 (Homo sapiens)
Go to Gene View: CD40
Go to UniProtKB:  P25942
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3H56-5 domain antibody (dAb)
B, E, G, I
121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.268 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 156.600α = 90.00
b = 158.300β = 90.00
c = 200.700γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-29 
  • 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
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Database references