4Y16

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4Y16

  • 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 the Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium dzajonc@lji.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1A285Mus musculusMutation(s): 1 
Gene Names: Cd1d1Cd1.1
Find proteins for P11609 (Mus musculus)
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Go to UniProtKB:  P11609
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
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NIH Common Fund Data Resources
IMPC  MGI:88127
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)C209Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav11
Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS  P01848
Find proteins for A0A0B4J1J9 (Mus musculus)
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Go to UniProtKB:  A0A0B4J1J9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)D241Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: TRBC2
Find proteins for A2NTY6 (Mus musculus)
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Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens)
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PHAROS  A0A5B9
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
48G
Query on 48G

Download Ideal Coordinates 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 Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.64α = 90
b = 191.914β = 90
c = 151.92γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI074952

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2016-07-27
    Changes: Data collection
  • Version 1.4: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2017-11-22
    Changes: Refinement description
  • Version 1.6: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary