Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


2 A crystal structure of an extracellular fragment of human CD40 ligand.

Karpusas, M.Hsu, Y.M.Wang, J.H.Thompson, J.Lederman, S.Chess, L.Thomas, D.

(1995) Structure 3: 1031-1039

  • DOI: https://doi.org/10.1016/s0969-2126(01)00239-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The CD40 ligand (CD40L) is a member of the tumor necrosis factor (TNF) family of proteins and is transiently expressed on the surface of activated T cells. The binding of CD40L to CD40, which is expressed on the surface of B cells, provides a critical and unique pathway of cellular activation resulting in antibody isotype switching, regulation of apoptosis, and B cell proliferation and differentiation. Naturally occurring mutations of CD40L result in the clinical hyper-IgM syndrome, characterized by an inability to produce immunoglobulins of the IgG, IgA and IgE isotypes. We have determined the crystal structure of a soluble extracellular fragment of human CD40L to 2 A resolution and with an R factor of 21.8%. Although the molecule forms a trimer similar to that found for other members of the TNF family, such as TNF alpha and lymphotoxin-alpha, and exhibits a similar overall fold, there are considerable differences in several loops including those predicted to be involved in CD40 binding. The structure suggests that most of the hyper-IgM syndrome mutations affect the folding and stability of the molecule rather than the CD40-binding site directly. Despite the fact that the hyper-IgM syndrome mutations are dispersed in the primary sequence, a large fraction of them are clustered in space in the vicinity of a surface loop, close to the predicted CD40-binding site.

  • Organizational Affiliation

    Biogen, Inc., Cambridge, MA 02142, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD40 LIGAND146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P29965 (Homo sapiens)
Explore P29965 
Go to UniProtKB:  P29965
PHAROS:  P29965
GTEx:  ENSG00000102245 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29965
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.17α = 90
b = 77.17β = 90
c = 90.46γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
BUDDHAdata reduction
X-PLORmodel building
XDSdata reduction
BUDDHAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description