2PKD

Crystal structure of CD84: Insite into SLAM family function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.043 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of CD84 provides insight into SLAM family function.

Yan, Q.Malashkevich, V.N.Fedorov, A.Fedorov, E.Cao, E.Lary, J.W.Cole, J.L.Nathenson, S.G.Almo, S.C.

(2007) Proc.Natl.Acad.Sci.Usa 104: 10583-10588

  • DOI: 10.1073/pnas.0703893104

  • PubMed Abstract: 
  • The signaling lymphocyte activation molecule (SLAM) family includes homophilic and heterophilic receptors that modulate both adaptive and innate immune responses. These receptors share a common ectodomain organization: a membrane-proximal immunoglobu ...

    The signaling lymphocyte activation molecule (SLAM) family includes homophilic and heterophilic receptors that modulate both adaptive and innate immune responses. These receptors share a common ectodomain organization: a membrane-proximal immunoglobulin constant domain and a membrane-distal immunoglobulin variable domain that is responsible for ligand recognition. CD84 is a homophilic family member that enhances IFN-gamma secretion in activated T cells. Our solution studies revealed that CD84 strongly self-associates with a K(d) in the submicromolar range. These data, in combination with previous reports, demonstrate that the SLAM family homophilic affinities span at least three orders of magnitude and suggest that differences in the affinities may contribute to the distinct signaling behavior exhibited by the individual family members. The 2.0 A crystal structure of the human CD84 immunoglobulin variable domain revealed an orthogonal homophilic dimer with high similarity to the recently reported homophilic dimer of the SLAM family member NTB-A. Structural and chemical differences in the homophilic interfaces provide a mechanism to prevent the formation of undesired heterodimers among the SLAM family homophilic receptors. These structural data also suggest that, like NTB-A, all SLAM family homophilic dimers adopt a highly kinked organization spanning an end-to-end distance of approximately 140 A. This common molecular dimension provides an opportunity for all two-domain SLAM family receptors to colocalize within the immunological synapse and bridge the T cell and antigen-presenting cell.


    Organizational Affiliation

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SLAM family member 5
A, B, C, D, E, F
111Homo sapiensMutation(s): 0 
Gene Names: CD84 (SLAMF5)
Find proteins for Q9UIB8 (Homo sapiens)
Go to Gene View: CD84
Go to UniProtKB:  Q9UIB8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.043 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.013α = 90.00
b = 170.982β = 90.00
c = 148.527γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
CBASSdata collection
SHELXphasing
RESOLVEphasing
SHELXSphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2007-12-17
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description