3QD6

Crystal structure of the CD40 and CD154 (CD40L) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD40 ligand
A, B, C, D, E, F
149Homo sapiensMutation(s): 0 
Gene Names: CD40LG (CD40L, TNFSF5, TRAP)
Find proteins for P29965 (Homo sapiens)
Go to Gene View: CD40LG
Go to UniProtKB:  P29965
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 5
R, S, T, U
177Homo sapiensMutation(s): 0 
Gene Names: CD40 (TNFRSF5)
Find proteins for P25942 (Homo sapiens)
Go to Gene View: CD40
Go to UniProtKB:  P25942
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 133.212α = 90.00
b = 133.212β = 90.00
c = 211.151γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
CNSrefinement
MOSFLMdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references