3JVG

Crystal Structure of chicken CD1-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for lipid-antigen recognition in avian immunity.

Dvir, H.Wang, J.Ly, N.Dascher, C.C.Zajonc, D.M.

(2010) J.Immunol. 184: 2504-2511

  • DOI: 10.4049/jimmunol.0903509

  • PubMed Abstract: 
  • CD1 proteins present self- and foreign lipid Ags to activate specific T cells in the mammalian immune system. These T cells play an important role in controlling autoimmune diseases, suppression of tumor growth, and host defense against invading path ...

    CD1 proteins present self- and foreign lipid Ags to activate specific T cells in the mammalian immune system. These T cells play an important role in controlling autoimmune diseases, suppression of tumor growth, and host defense against invading pathogens. Humans use five CD1 isoforms, whereas only two exist in birds. Unlike mammals' CD1, the structure of chicken CD1-2 showed a primitive lipid-binding groove, suggesting that chicken may only recognize single-chain lipids. In contrast, the crystal structure of the second chicken CD1 isoform, chCD1-1, reported in this study at 2.2 A resolution, reveals an elaborated binding groove with a dual-pocket, dual-cleft architecture. The A' and F' deep pockets are separated from each other, but each is connected to a hydrophobic surface cleft, which may participate in lipid binding. The long endogenous ligand found inside the binding groove of chCD1-1, together with binding data on various glycolipids and mycolic acid, strongly suggest that the unique avian CD1 family could bind long dual- and possibly triacyl-chain lipids.


    Organizational Affiliation

    Department of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1A1 antigen
A, B
281Gallus gallusMutation(s): 0 
Gene Names: CD1A1
Find proteins for A5HUM9 (Gallus gallus)
Go to UniProtKB:  A5HUM9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
C, D
98Gallus gallusMutation(s): 0 
Gene Names: B2M
Find proteins for P21611 (Gallus gallus)
Go to Gene View: B2M
Go to UniProtKB:  P21611
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.839α = 90.00
b = 112.124β = 90.00
c = 201.773γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance