3QD6

Crystal structure of the CD40 and CD154 (CD40L) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic and mutational analysis of the CD40-CD154 complex and its implications for receptor activation

An, H.-J.Kim, Y.J.Song, D.H.Park, B.S.Kim, H.M.Lee, J.D.Paik, S.-G.Lee, J.-O.Lee, H.

(2011) J Biol Chem 286: 11226-11235

  • DOI: 10.1074/jbc.M110.208215
  • Primary Citation of Related Structures:  
    3QD6

  • PubMed Abstract: 
  • CD40 is a tumor necrosis factor receptor (TNFR) family protein that plays an important role in B cell development. CD154/CD40L is the physiological ligand of CD40. We have determined the crystal structure of the CD40-CD154 complex at 3.5 Å resolution ...

    CD40 is a tumor necrosis factor receptor (TNFR) family protein that plays an important role in B cell development. CD154/CD40L is the physiological ligand of CD40. We have determined the crystal structure of the CD40-CD154 complex at 3.5 Å resolution. The binding site of CD40 is located in a crevice formed between two CD154 subunits. Charge complementarity plays a critical role in the CD40-CD154 interaction. Some of the missense mutations found in hereditary hyper-IgM syndrome can be mapped to the CD40-CD154 interface. The CD40 interaction area of one of the CD154 subunits is twice as large as that of the other subunit forming the binding crevice. This is because cysteine-rich domain 3 (CRD3) of CD40 has a disulfide bridge in an unusual position that alters the direction of the ladder-like structure of CD40. The Ser(132) loop of CD154 is not involved in CD40 binding but its substitution significantly reduces p38- and ERK-dependent signaling by CD40, whereas JNK-dependent signaling is not affected. These findings suggest that ligand-induced di- or trimerization is necessary but not sufficient for complete activation of CD40.


    Organizational Affiliation

    Department of Biology, College of Bioscience & Biotechnology, Chungnam National University, Daejon, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CD40 ligandABCDEF149Homo sapiensMutation(s): 0 
Gene Names: CD154CD40LCD40LGTNFSF5TRAP
Find proteins for P29965 (Homo sapiens)
Explore P29965 
Go to UniProtKB:  P29965
NIH Common Fund Data Resources
PHAROS  P29965
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 5RSTU177Homo 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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D, E, F
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.212α = 90
b = 133.212β = 90
c = 211.151γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary