3TVM

Structure of the mouse CD1d-SMC124-iNKT TCR complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report



Literature

Glycolipids that Elicit IFN-gama-Biased Responses from Natural Killer T Cells

Tyznik, A.J., Farber, E., Girardi, E., Birkholz, A., Li, Y., Chitale, S., So, R., Arora, P., Khurana, A., Wang, J., Porcelli, S.A., Zajonc, D.M., Kronenberg, M., Howell, A.R.

(2011) Chem Biol 18: 1620-1630

  • DOI: 10.1016/j.chembiol.2011.10.015
  • Primary Citation of Related Structures:  
    3TVM

  • PubMed Abstract: 

    • Natural killer T (NKT) cells recognize glycolipids presented by CD1d. The first antigen described, α-galactosyl ceramide (αGalCer), is a potential anticancer agent whose activity depends upon IFN-γ secretion. We report two analogs of αGalCer based on ...

    Natural killer T (NKT) cells recognize glycolipids presented by CD1d. The first antigen described, α-galactosyl ceramide (αGalCer), is a potential anticancer agent whose activity depends upon IFN-γ secretion. We report two analogs of αGalCer based on a naturally occurring glycosphingolipid, plakoside A. These compounds induce enhanced IFN-γ that correlates with detergent-resistant binding to CD1d and an increased stability of the lipid-CD1d complexes on antigen-presenting cells. Structural analysis on one of the analogs indicates that it is more deeply bound inside the CD1d groove, suggesting tighter lipid-CD1d interactions. To our knowledge, this is the first example in which structural information provides an explanation for the increased lipid-CD1d stability, likely responsible for the Th1 bias. We provide insights into the mechanism of IFN-γ-inducing compounds, and because our compounds activate human NKT cells, they could have therapeutic utility.

    Organizational Affiliation: 

    Division of Developmental Immunology, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1A, E285Mus musculusMutation(s): 1 
Gene Names: Cd1.1, CD1d, Cd1d1
Find proteins for P11609 (Mus musculus)
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Go to UniProtKB:  P11609
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
beta-2-microglobulinB, F99Mus musculusMutation(s): 1 
Gene Names: beta-2-microglobulin, 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
Valpha14 (mouse variable domain, human constant domain)C, G209Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Valpha14 (mouse variable domain
Find proteins for P01848 (Homo sapiens)
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PHAROS  P01848
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Vbeta8.2 (mouse variable domain, human constant domain)D, H241Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Vbeta8.2 (mouse variable domain
Find proteins for A0A5B9 (Homo sapiens)
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Go to UniProtKB:  A0A5B9
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PHAROS  A0A5B9
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  • Reference Sequence
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
I, K
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
J, L
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
07P
Query on 07P
Download CCD File 
A, E
N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide
C55 H107 N O8
BCHXWZQXEKOXKQ-IYKQKVLOSA-N		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
A, E
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
GOL
Query on GOL
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E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.97α = 90
b = 150.57β = 96.35
c = 101.96γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary