4Y16

Crystal structure of the mCD1d/NC-aGC/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Lipid and Carbohydrate Modifications of alpha-Galactosylceramide Differently Influence Mouse and Human Type I Natural Killer T Cell Activation.

Birkholz, A.Nemcovic, M.Yu, E.D.Girardi, E.Wang, J.Khurana, A.Pauwels, N.Farber, E.Chitale, S.Franck, R.W.Tsuji, M.Howell, A.Van Calenbergh, S.Kronenberg, M.Zajonc, D.M.

(2015) J.Biol.Chem. 290: 17206-17217

  • DOI: 10.1074/jbc.M115.654814

  • PubMed Abstract: 
  • The ability of different glycosphingolipids (GSLs) to activate type I natural killer T cells (NKT cells) has been known for 2 decades. The possible therapeutic use of these GSLs has been studied in many ways; however, studies are needed in which the ...

    The ability of different glycosphingolipids (GSLs) to activate type I natural killer T cells (NKT cells) has been known for 2 decades. The possible therapeutic use of these GSLs has been studied in many ways; however, studies are needed in which the efficacy of promising GSLs is compared under identical conditions. Here, we compare five unique GSLs structurally derived from α-galactosylceramide. We employed biophysical and biological assays, as well as x-ray crystallography to study the impact of the chemical modifications of the antigen on type I NKT cell activation. Although all glycolipids are bound by the T cell receptor of type I NKT cells in real time binding assays with high affinity, only a few activate type I NKT cells in in vivo or in vitro experiments. The differences in biological responses are likely a result of different pharmacokinetic properties of each lipid, which carry modifications at different parts of the molecule. Our results indicate a need to perform a variety of assays to ascertain the therapeutic potential of type I NKT cell GSL activators.


    Organizational Affiliation

    From the Division of Cell Biology and Division of Developmental Immunology,La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, the Division of Biological Sciences, University of California at San Diego, La Jolla, California 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A
285Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
C
209Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav11 (Trav11d), TRAC (TCRA)
Find proteins for A0A0B4J1J9 (Mus musculus)
Go to UniProtKB:  A0A0B4J1J9
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
D
241Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: TRBC2 (TCRBC2)
Find proteins for A2NTY6 (Mus musculus)
Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
48G
Query on 48G

Download SDF File 
Download CCD File 
A
N-[(2S,3S,4R)-3,4-dihydroxy-1-{[6-O-(naphthalen-1-ylcarbamoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide
C61 H106 N2 O10
FWXGYYGDUQYCLV-DBQLOCGYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download SDF File 
Download CCD File 
A
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.640α = 90.00
b = 191.914β = 90.00
c = 151.920γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI074952

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Database references
  • Version 1.2: 2015-07-22
    Type: Database references
  • Version 1.3: 2016-07-27
    Type: Data collection
  • Version 1.4: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.5: 2017-11-22
    Type: Refinement description