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 CD1d1AE285Mus musculusMutation(s): 1 
Gene Names: Cd1.1CD1dCd1d1
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-microglobulinBF99Mus musculusMutation(s): 1 
Gene Names: beta-2-microglobulinB2m
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Valpha14 (mouse variable domain, human constant domain)CG209Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Valpha14 (mouse variable domain
Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
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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)DH241Mus musculusHomo 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
NIH Common Fund Data Resources
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

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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

View Full Validation Report



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