Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 97.43 kDa 
• Atom Count: 7014 
• Residue Count: 809 
• Unique protein chains: 4

6MJI

Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex

• DOI: 10.2210/pdb6MJI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-09-20 Released: 2019-01-09 
• Deposition Author(s): Zajonc, D.M., Bitra, A., Janssens, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

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

• PubMed: 30556652 
• DOI: 10.1002/cmdc.201800649
• Primary Citation of Related Structures:  
  6MJQ, 6MJJ, 6MJI, 6MJA, 6MJ4, 6MJ6, 6MIV, 6MIY


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN	C	209	Mus musculus, Homo sapiens	Mutation(s): 0  Gene Names: Trav11, Trav11d
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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-chain,Tcell receptor chain,T cell receptor beta constant 2	D	241	Mus musculus, Homo sapiens	Mutation(s): 2
Find proteins for A0N8J3 (Mus musculus) Explore A0N8J3  Go to UniProtKB:  A0N8J3
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6  Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9  Go to UniProtKB:  A0A5B9
NIH Common Fund Data Resources
PHAROS  A0A5B9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 0  Gene Names: Cd1d1, mCG_3074, Cd1.1
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JTD	A	N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide C54 H105 N O9 CVKVQMALSPWMOL-KGOGAPLFSA-N
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	A, B, D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.216	α = 90
b = 191.161	β = 90
c = 151.095	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-09-20 
• Released Date: 2019-01-09 
Deposition Author(s): Zajonc, D.M., Bitra, A., Janssens, J.

Revision History 

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary