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 

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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 efficacy of promising GSLs is compared under identical conditions ...

    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: Cd1d1, Cd1.1
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Find proteins for P11609 (Mus musculus)
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Go to UniProtKB:  P11609
IMPC:  MGI:107674
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UniProt GroupP11609
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Mus musculusMutation(s): 0 
Gene Names: B2m
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Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)C209Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Trav11, Trav11d
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Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
PHAROS:  P01848
Find proteins for A0A0B4J1J9 (Mus musculus)
Explore A0A0B4J1J9 
Go to UniProtKB:  A0A0B4J1J9
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UniProt GroupsA0A0B4J1J9P01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)D241Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: TRBC2, TCRBC2
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Find proteins for A2NTY6 (Mus musculus)
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Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens)
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Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9
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UniProt GroupsA0A5B9A2NTY6
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G28454KX
GlyCosmos:  G28454KX
GlyGen:  G28454KX
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
48G
Query on 48G
Download Ideal Coordinates CCD File 
G [auth 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 
H [auth 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

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • 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