Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20601.23 
• Atom Count: 1453 
• Residue Count: 171 
• Unique protein chains: 1

1CCZ

CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3) AT 1.8-A RESOLUTION

• DOI: 10.2210/pdb1CCZ/pdb

• Classification: GLYCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• Deposited: 1999-03-02 Released: 1999-04-05 
• Deposition Author(s): Ikemizu, S., Sparks, L.M., Van Der Merwe, P.A., Harlos, K., Stuart, D.I., Jones, E.Y., Davis, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.243 
• R-Value Work: 0.202 

Literature

Crystal structure of the CD2-binding domain of CD58 (lymphocyte function-associated antigen 3) at 1.8-A resolution.

Ikemizu, S., Sparks, L.M., van der Merwe, P.A., Harlos, K., Stuart, D.I., Jones, E.Y., Davis, S.J.

(1999) Proc.Natl.Acad.Sci.USA 96: 4289-4294

• PubMed: 10200255 


• PubMed Abstract: 
  

The binding of the cell surface molecule CD58 (formerly lymphocyte function-associated antigen 3) to its ligand, CD2, significantly increases the sensitivity of antigen recognition by T cells. This was the first heterophilic cell adhesion interaction to be discovered and is now an important paradigm for analyzing the structural basis of cell-cell recognition. The crystal structure of a CD2-binding chimeric form of CD58, solved to 1.8-A resolution, reveals that the ligand binding domain of CD58 has the expected Ig superfamily V-set topology and shares several of the hitherto unique structural features of CD2, consistent with previous speculation that the genes encoding these molecules arose via duplication of a common precursor. Nevertheless, evidence for considerable divergence of CD2 and CD58 is also implicit in the structures. Mutations that disrupt CD2 binding map to the highly acidic surface of the AGFCC'C" beta-sheet of CD58, which, unexpectedly, lacks marked shape complementarity to the equivalent, rather more basic CD58-binding face of human CD2. The specificity of the very weak interactions of proteins mediating cell-cell recognition may often derive largely from electrostatic complementarity, with shape matching at the protein-protein interface being less exact than for interactions that combine specificity with high affinity, such as those involving antibodies.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, the Rex Richards Building, South Parks Road, Oxford, OX1 3QU, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (CD58)	A	171	Homo sapiens	Mutation(s): 0  Gene Names: CD58 (LFA3)
Find proteins for P19256 (Homo sapiens) Go to Gene View: CD58 Go to UniProtKB:  P19256

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.243 
• R-Value Work: 0.202 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 116.430	α = 90.00
b = 116.430	β = 90.00
c = 51.520	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
SCALEPACK	data scaling
X-PLOR	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-03-02 
• Released Date: 1999-04-05 
• Deposition Author(s): Ikemizu, S., Sparks, L.M., Van Der Merwe, P.A., Harlos, K., Stuart, D.I., Jones, E.Y., Davis, S.J.

Revision History 

• Version 1.0: 1999-04-05
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance