2GAZ

Mycobacterial lipoglycan presentation by CD1d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of mycobacterial phosphatidylinositol mannoside binding to mouse CD1d.

Zajonc, D.M.Ainge, G.D.Painter, G.F.Severn, W.B.Wilson, I.A.

(2006) J Immunol 177: 4577-4583

  • DOI: 10.4049/jimmunol.177.7.4577
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mycobacterial phosphatidylinositol tetramannosides (PIM4) are agonists for a distinct population of invariant human (Valpha24) and mouse (Valpha14) NKT cells, when presented by CD1d. We determined the crystal structure at 2.6-A resolution of mouse CD ...

    Mycobacterial phosphatidylinositol tetramannosides (PIM4) are agonists for a distinct population of invariant human (Valpha24) and mouse (Valpha14) NKT cells, when presented by CD1d. We determined the crystal structure at 2.6-A resolution of mouse CD1d bound to a synthetic dipalmitoyl-PIM2. Natural PIM2, which differs in its fatty acid composition is a biosynthetic precursor of PIM4, PIM6, lipomannan, and lipoarabinomannan. The PIM2 headgroup (inositol-dimannoside) is the most complex to date among all the crystallized CD1d ligands and is remarkably ordered in the CD1d binding groove. A specific hydrogen-bonding network between PIM2 and CD1d orients the headgroup in the center of the binding groove and above the A' pocket. A central cluster of hydrophilic CD1d residues (Asp(153), Thr(156), Ser(76), Arg(79)) interacts with the phosphate, inositol, and alpha1-alpha6-linked mannose of the headgroup, whereas additional specificity for the alpha1- and alpha2-linked mannose is conferred by Thr(159). The additional two mannoses in PIM4, relative to PIM2, are located at the distal 6' carbon of the alpha1-alpha6-linked mannose and would project away from the CD1d binding groove for interaction with the TCR. Compared with other CD1d-sphingolipid structures, PIM2 has an increased number of polar interactions between its headgroup and CD1, but reduced specificity for the diacylglycerol backbone. Thus, novel NKT cell agonists can be designed that focus on substitutions of the headgroup rather than on reducing lipid chain length, as in OCH and PBS-25, two potent variants of the highly stimulatory invariant NKT cell agonist alpha-galactosylceramide.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1d1
A
285Mus musculusMutation(s): 0 
Gene Names: Cd1d1Cd1.1
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
beta-2-microglobulin
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XPX
Query on XPX

Download CCD File 
A
(2R)-3-[(HYDROXY{[(2R,3R,5S,6R)-3,4,5-TRIHYDROXY-2,6-BIS(ALPHA-D-MANNOPYRANOSYLOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]PROPANE-1,2-DIYL DIHEXADECANOATE
C53 H99 O23 P
XGAHMXUNNQXCDP-FKPQOHGQSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.835α = 90
b = 110.757β = 90
c = 107.396γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-03-09 
  • Released Date: 2006-09-26 
  • Deposition Author(s): Zajonc, D.M.

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance