Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63945.46 
• Atom Count: 4290 
• Residue Count: 574 
• Unique protein chains: 3

1YJD

Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)

• DOI: 10.2210/pdb1YJD/pdb

• Classification: IMMUNE SYSTEM/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• Deposited: 2005-01-14 Released: 2005-02-15 
• Deposition Author(s): Evans, E.J., Esnouf, R.M., Manso-Sancho, R., Gilbert, R.J.C., James, J.R., Sorensen, P., Stuart, D.I., Davis, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.282 
• R-Value Work: 0.239 

Literature

Crystal structure of a soluble CD28-Fab complex

Evans, E.J., Esnouf, R.M., Manso-Sancho, R., Gilbert, R.J.C., James, J.R., Yu, C., Fennelly, J.A., Vowles, C., Hanke, T., Walse, B., Hunig, T., Sorensen, P., Stuart, D.I., Davis, S.J.

(2005) Nat.Immunol. 6: 271-279

• PubMed: 15696168 
• DOI: 10.1038/ni1170


• PubMed Abstract: 
  

Naive T cell activation requires signaling by the T cell receptor and by nonclonotypic cell surface receptors. The most important costimulatory protein is the monovalent homodimer CD28, which interacts with CD80 and CD86 expressed on antigen-presenting cells. Here we present the crystal structure of a soluble form of CD28 in complex with the Fab fragment of a mitogenic antibody. Structural comparisons redefine the evolutionary relationships of CD28-related proteins, antigen receptors and adhesion molecules and account for the distinct ligand-binding and stoichiometric properties of CD28 and the related, inhibitory homodimer CTLA-4. Cryo-electron microscopy-based comparisons of complexes of CD28 with mitogenic and nonmitogenic antibodies place new constraints on models of antibody-induced receptor triggering. This work completes the initial structural characterization of the CD28-CTLA-4-CD80-CD86 signaling system.

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Organizational Affiliation: 

Nuffield Department of Clinical Medicine, The University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab fragment of 5.11A1 antibody light chain	L	212	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab fragment of 5.11A1 antibody heavy chain	H	222	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
T-cell-specific surface glycoprotein CD28	C	140	Homo sapiens	Mutation(s): 0  Gene Names: CD28
Find proteins for P10747 (Homo sapiens) Go to Gene View: CD28 Go to UniProtKB:  P10747

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.282 
• R-Value Work: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 191.219	α = 90.00
b = 47.417	β = 94.45
c = 71.842	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	refinement
X-PLOR	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-14 
• Released Date: 2005-02-15 
• Deposition Author(s): Evans, E.J., Esnouf, R.M., Manso-Sancho, R., Gilbert, R.J.C., James, J.R., Sorensen, P., Stuart, D.I., Davis, S.J.

Revision History 

• Version 1.0: 2005-02-15
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance