3QUX

Structure of the mouse CD1d-alpha-C-GalCer-iNKT TCR complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report



Literature

Galactose-modified iNKT cell agonists stabilized by an induced fit of CD1d prevent tumour metastasis.

Aspeslagh, S., Li, Y., Yu, E.D., Pauwels, N., Trappeniers, M., Girardi, E., Decruy, T., Van Beneden, K., Venken, K., Drennan, M., Leybaert, L., Wang, J., Franck, R.W., Van Calenbergh, S., Zajonc, D.M., Elewaut, D.

(2011) EMBO J 30: 2294-2305

  • DOI: 10.1038/emboj.2011.145
  • Primary Citation of Related Structures:  
    3QUX, 3QUY, 3QUZ

  • PubMed Abstract: 

    • Invariant natural killer T (iNKT) cells are known to have marked immunomodulatory capacity due to their ability to produce copious amounts of effector cytokines. Here, we report the structure and function of a novel class of aromatic α-galactosylcera ...

    Invariant natural killer T (iNKT) cells are known to have marked immunomodulatory capacity due to their ability to produce copious amounts of effector cytokines. Here, we report the structure and function of a novel class of aromatic α-galactosylceramide structurally related glycolipids with marked Th1 bias in both mice and men, leading to superior tumour protection in vivo. The strength of the Th1 response correlates well with enhanced lipid binding to CD1d as a result of an induced fit mechanism that binds the aromatic substitution as a third anchor, in addition to the two lipid chains. This induced fit is in contrast to another Th1-biasing glycolipid, α-C-GalCer, whose CD1d binding follows a conventional key-lock principle. These findings highlight the previously unexploited flexibility of CD1d in accommodating galactose-modified glycolipids and broaden the range of glycolipids that can stimulate iNKT cells. We speculate that glycolipids can be designed that induce a similar fit, thereby leading to superior and more sustained iNKT cell responses in vivo.

    Organizational Affiliation: 

    Department of Rheumatology, Faculty of Medicine and Health Sciences, Laboratory for Molecular Immunology and Inflammation, Ghent University, Ghent, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1A285Mus musculusMutation(s): 0 
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 microglobulinB99Mus musculusMutation(s): 0 
Gene Names: B2m, beta-2-microglobulin, mCG_11606, RP23-34E24.5-001
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)C209Mus musculusMutation(s): 0 
Find proteins for P01848 (Homo sapiens)
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PHAROS  P01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Vbeta8.2 (mouse variable domain, human constant domain)D241Mus musculusMutation(s): 0 
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUX
Query on QUX
Download Ideal Coordinates CCD File 
A
N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide
C51 H101 N O8
BNYLLEHBKIGJHB-XHSUSRKPSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QUXKd :  247   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.502α = 90
b = 189.919β = 90
c = 150.801γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary