1E87

Human CD69 - trigonal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the C-Type Lectin-Like Domain from the Human Hematopoietic Cell Receptor Cd69

Llera, A.S.Viedma, F.Sanchez-Madrid, F.Tormo, J.

(2001) J.Biol.Chem. 276: 7312

  • DOI: 10.1074/jbc.M008573200
  • Primary Citation of Related Structures:  1E8I

  • PubMed Abstract: 
  • CD69, one of the earliest specific antigens acquired during lymphoid activation, acts as a signal-transducing receptor involved in cellular activation events, including proliferation and induction of specific genes. CD69 belongs to a family of recept ...

    CD69, one of the earliest specific antigens acquired during lymphoid activation, acts as a signal-transducing receptor involved in cellular activation events, including proliferation and induction of specific genes. CD69 belongs to a family of receptors that modulate the immune response and whose genes are clustered in the natural killer (NK) gene complex. The extracellular portion of these receptors represent a subfamily of C-type lectin-like domains (CTLDs), which are divergent from true C-type lectins and are referred to as NK-cell domains (NKDs). We have determined the three-dimensional structure of human CD69 NKD in two different crystal forms. CD69 NKD adopts the canonical CTLD fold but lacks the features involved in Ca(2+) and carbohydrate binding by C-type lectins. CD69 NKD dimerizes noncovalently, both in solution and in crystalline state. The dimer interface consists of a hydrophobic, loosely packed core, surrounded by polar interactions, including an interdomain beta sheet. The intersubunit core shows certain structural plasticity that may facilitate conformational rearrangements for binding to ligands. The surface equivalent to the binding site of other members of the CTLD superfamily reveals a hydrophobic patch surrounded by conserved charged residues that probably constitutes the CD69 ligand-binding site.


    Organizational Affiliation

    Department of Macromolecular Structure, Centro Nacional de Biotecnologia, Universidad Autónoma de Madrid, 28049 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EARLY ACTIVATION ANTIGEN CD69
A
118Homo sapiensGene Names: CD69 (CLEC2C)
Find proteins for Q07108 (Homo sapiens)
Go to Gene View: CD69
Go to UniProtKB:  Q07108
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.424α = 90.00
b = 48.424β = 90.00
c = 119.886γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-09-18 
  • Released Date: 2000-09-26 
  • Deposition Author(s): Tormo, J.

Revision History 

  • Version 1.0: 2000-09-26
    Type: Initial release
  • Version 1.1: 2011-08-24
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance