3DBX

Structure of chicken CD1-2 with bound fatty acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of avian CD1 reveals a smaller, more primordial antigen-binding pocket compared to mammalian CD1

Zajonc, D.M.Striegl, H.Dascher, C.C.Wilson, I.A.

(2008) Proc.Natl.Acad.Sci.Usa 105: 17925-17930

  • DOI: 10.1073/pnas.0809814105

  • PubMed Abstract: 
  • The molecular details of glycolipid presentation by CD1 antigen-presenting molecules are well studied in mammalian systems. However, little is known about how these non-classical MHC class I (MHCI) molecules diverged from the MHC locus to create a mo ...

    The molecular details of glycolipid presentation by CD1 antigen-presenting molecules are well studied in mammalian systems. However, little is known about how these non-classical MHC class I (MHCI) molecules diverged from the MHC locus to create a more complex, hydrophobic binding groove that binds lipids rather than peptides. To address this fundamental question, we have determined the crystal structure of an avian CD1 (chCD1-2) that shares common ancestry with mammalian CD1 from approximately 310 million years ago. The chCD1-2 antigen-binding site consists of a compact, narrow, central hydrophobic groove or pore rather than the more open, 2-pocket architecture observed in mammalian CD1s. Potential antigens then would be restricted in size to single-chain lipids or glycolipids. An endogenous ligand, possibly palmitic acid, serves to illuminate the mode and mechanism of ligand interaction with chCD1-2. The palmitate alkyl chain is inserted into the relatively shallow hydrophobic pore; its carboxyl group emerges at the receptor surface and is stabilized by electrostatic and hydrogen bond interactions with an arginine residue that is conserved in all known CD1 proteins. In addition, other novel features, such as an A' loop that interrupts and segments the normally long, continuous alpha1 helix, are unique to chCD1-2 and contribute to the unusually narrow binding groove, thereby limiting its size. Because birds and mammals share a common ancestor, but the rate of evolution is slower in birds than in mammals, the chCD1-2-binding groove probably represents a more primordial CD1-binding groove.


    Organizational Affiliation

    Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA. dzajonc@liai.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD1-2 antigen
A
289Gallus gallusMutation(s): 0 
Find proteins for Q5GL29 (Gallus gallus)
Go to UniProtKB:  Q5GL29
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.154α = 90.00
b = 92.154β = 90.00
c = 96.693γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance