5TW2 | pdb_00005tw2

Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168

• PDB DOI: https://doi.org/10.2210/pdb5TW2/pdb

• Classification: immune system/inhibitor
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-11-11 Released: 2017-09-20 
• Deposition Author(s): Zajonc, D.M., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.221 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Galactosylsphingamides: new alpha-GalCer analogues to probe the F'-pocket of CD1d.

Guillaume, J., Wang, J., Janssens, J., Remesh, S.G., Risseeuw, M.D.P., Decruy, T., Froeyen, M., Elewaut, D., Zajonc, D.M., Calenbergh, S.V.

(2017) Sci Rep 7: 4276-4276

• PubMed: 28655912 
• DOI: https://doi.org/10.1038/s41598-017-04461-7
• Primary Citation Related Structures: 
  5TW2, 5TW5


• PubMed Abstract: 
  

  Invariant Natural Killer T-cells (iNKT-cells) are an attractive target for immune response modulation, as upon CD1d-mediated stimulation with KRN7000, a synthetic α-galactosylceramide, they produce a vast amount of cytokines. Here we present a synthesis that allows swift modification of the phytosphingosine side chain by amidation of an advanced methyl ester precursor. The resulting KRN7000 derivatives, termed α-galactosylsphingamides, were evaluated for their capacity to stimulate iNKT-cells. While introduction of the amide-motif in the phytosphingosine chain is tolerated for CD1d binding and TCR recognition, the studied α-galactosylsphingamides showed compromised antigenic properties.

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Organizational Affiliation: 
• Laboratory for Medicinal Chemistry (FFW), Faculty of Pharmaceutical Sciences, UGent, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.
Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000, Ghent, Belgium.
Unit Molecular Immunology and Inflammation, VIB Inflammation Research Center, Ghent University, Ghent, Belgium.
KU Leuven, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium.
Laboratory for Medicinal Chemistry (FFW), Faculty of Pharmaceutical Sciences, UGent, Ottergemsesteenweg 460, B-9000, Ghent, Belgium. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 46 kDa 
• Atom Count: 3,384 
• Modeled Residue Count: 365 
• Deposited Residue Count: 384 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 1  Gene Names: Cd1d1, Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609
IMPC:  MGI:107674
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P11609-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Mus musculus	Mutation(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

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7LP	E [auth A]	(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide C34 H58 N2 O10 GAPCJLRKOKSZTA-RMRXMYJTSA-N
PLM	F [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.221 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.203	α = 90
b = 107.466	β = 90
c = 109.55	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Zajonc, D.M., Wang, J.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary