Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 96.44 kDa 
• Atom Count: 6861 
• Modelled Residue Count: 807 
• Deposited Residue Count: 834 
• Unique protein chains: 4

3QUY

Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex

• DOI: 10.2210/pdb3QUY/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-24 Released: 2011-06-29 
• Deposition Author(s): Li, Y., Girardi, E., Yu, E.D., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

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

• PubMed: 21552205 
• 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 0  Gene Names: Cd1.1, CD1d, Cd1d1
UniProt
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2 microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m, beta-2-microglobulin, mCG_11606, RP23-34E24.5-001
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Valpha14 (mouse variable domain, human constant domain)	C	209	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vbeta8.2 (mouse variable domain, human constant domain)	D	241	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUY (Subject of Investigation/LOI)	H [auth A]	(2S,3R,4S,5R,6S)-6-[(2S,3S,4R)-2-(hexacosanoylamino)-3,4-dihydroxy-octadecoxy]-3,4,5-trihydroxy-N-(phenylmethyl)oxane-2-carboxamide C57 H104 N2 O9 VILJJKVIHWALNM-YERUKUFISA-N
NAG (Subject of Investigation/LOI)	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QUY	PDBBind:  3QUY	Kd: 187 (nM) from 1 assay(s)
	Binding MOAD:  3QUY	Kd: 187 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.765	α = 90
b = 192.005	β = 90
c = 150.922	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2011-02-24 
• Released Date: 2011-06-29 
Deposition Author(s): Li, Y., Girardi, E., Yu, E.D., Zajonc, D.M.

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: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary