6MIV | pdb_00006miv

Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.219 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JU1Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.

Janssens, J.Bitra, A.Wang, J.Decruy, T.Venken, K.van der Eycken, J.Elewaut, D.Zajonc, D.M.van Calenbergh, S.

(2019) ChemMedChem 14: 147-168

  • DOI: https://doi.org/10.1002/cmdc.201800649
  • Primary Citation of Related Structures:  
    6MIV, 6MIY, 6MJ4, 6MJ6, 6MJA, 6MJI, 6MJJ, 6MJQ

  • PubMed Abstract: 

    Invariant natural killer T-cells (iNKT) are a glycolipid-responsive subset of T-lymphocytes that fulfill a pivotal role in the immune system. The archetypical synthetic glycolipid, α-galactosylceramide (α-GalCer), whose molecular framework is inspired by a group of amphiphilic natural products, remains the most studied antigen for iNKT-cells. Nonetheless, the potential of α-GalCer as an immunostimulating agent is compromised by the fact that this glycolipid elicits simultaneous secretion of Th1- and Th2-cytokines. This has incited medicinal chemistry efforts to identify analogues that are able to perturb the Th1/Th2 balance. In this work, we present the synthesis of an extensive set of 4"-O-alkylated α-GalCer analogues, which were evaluated in vivo for their cytokine induction. We have found that conversion of the 4"-OH group to ether moieties decreases the immunogenic potential in mice relative to α-GalCer. Yet, the benzyl-modified glycolipids are able to produce a distinct pro-inflammatory immune response. The crystal structures suggest an extra hydrophobic interaction between the benzyl moiety and the α2-helix of CD1d.


  • Organizational Affiliation

    Laboratory for Medicinal Chemistry, Department of Pharmaceutics (FFW), Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chainA [auth C]209Mus musculusHomo sapiensMutation(s): 0 
Gene Names: Trav11Trav11dTraj18B2MHDCMA22P
UniProt
Find proteins for A0A0B4J1J9 (Mus musculus)
Explore A0A0B4J1J9 
Go to UniProtKB:  A0A0B4J1J9
Find proteins for K7N5M3 (Homo sapiens)
Explore K7N5M3 
Go to UniProtKB:  K7N5M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsK7N5M3A0A0B4J1J9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-chain,Tcell receptor chain,T cell receptor beta constant 2B [auth D]241Mus musculusHomo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for A0N8J3 (Mus musculus)
Explore A0N8J3 
Go to UniProtKB:  A0N8J3
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0N8J3A0A5B9A2NTY6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1C [auth A]285Mus musculusMutation(s): 0 
Gene Names: Cd1d1mCG_3074
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus)
Explore P11609 
Go to UniProtKB:  P11609
IMPC:  MGI:107674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11609
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P11609-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth B]99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains 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
F
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JU1
Query on JU1

Download Ideal Coordinates CCD File 
M [auth A]N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide
C61 H113 N O9
SSSKPQWRYUMYKD-XRRYKDCJSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth C],
J [auth D],
N [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth C],
I [auth D],
K [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.976α = 90
b = 191.441β = 90
c = 151.369γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JU1Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary