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: 96.61 kDa 
• Atom Count: 6511 
• Residue Count: 805 
• Unique protein chains: 4

5VCJ

Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR

• DOI: 10.2210/pdb5VCJ/pdb

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


• Deposited: 2017-03-31 Released: 2018-04-04 
• Deposition Author(s): Wang, J., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.248 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Enhancing T cell responses and tumour immunity by vaccination with peptides conjugated to a weak NKT cell agonist.

Compton, B.J., Farrand, K.J., Tang, C.W., Osmond, T.L., Speir, M., Authier-Hall, A., Wang, J., Ferguson, P.M., Chan, S.T.S., Anderson, R.J., Cooney, T.R., Hayman, C.M., Williams, G.M., Brimble, M.A., Brooks, C.R., Yong, L.K., Metelitsa, L.S., Zajonc, D.M., Godfrey, D.I., Gasser, O., Weinkove, R., Painter, G.F., Hermans, I.F.

(2019) Org Biomol Chem 17: 1225-1237

• PubMed: 30656346 
• DOI: 10.1039/c8ob02982b
• Primary Citation of Related Structures:  
  5VCJ


• PubMed Abstract: 
  

Activated NKT cells can stimulate antigen-presenting cells leading to enhanced peptide antigen-specific immunity. However, administration of potent NKT cell agonists like α-galactosylceramide (α-GalCer) can be associated with release of high levels of cytokines, and in some situations, hepatotoxicity. Here we show that it is possible to provoke sufficient NKT cell activity to stimulate strong antigen-specific T cell responses without these unwanted effects. This was achieved by chemically conjugating antigenic peptides to α-galactosylphytosphingosine (α-GalPhs), an NKT cell agonist with very weak activity based on structural characterisation and biological assays. Conjugation improved delivery to antigen-presenting cells in vivo, while use of a cathepsin-sensitive linker to release the α-GalPhs and peptide within the same cell promoted strong T cell activation and therapeutic anti-tumour responses in mice. The conjugates activated human NKT cells and enhanced human T cell responses to a viral peptide in vitro. Accordingly, we have demonstrated a means to safely exploit the immunostimulatory properties of NKT cells to enhance T cell activation for virus- and tumour-specific immunity.

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Organizational Affiliation: 

The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand. [e-mail].

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
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
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)	C	209	Mus musculus, Homo sapiens This entity is chimeric	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)	D	241	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	E	6		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N57	A	(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside C24 H49 N O8 CBKONJDETAETLR-MKQNOXKVSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG	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: 3.16 Å
• R-Value Free: 0.248 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.261	α = 90
b = 191.611	β = 90
c = 151.249	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-31 
• Released Date: 2018-04-04 
Deposition Author(s): Wang, J., Zajonc, D.M.

Revision History 

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 2.0: 2019-05-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary