Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 196.11 kDa 
• Atom Count: 12603 
• Modelled Residue Count: 1589 
• Deposited Residue Count: 1700 
• Unique protein chains: 4

6BNL

Crystal structure of TCR-MHC-like molecule

• PDB DOI: 10.2210/pdb6BNL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-04-04 
• Deposition Author(s): Le Nours, J., Rossjohn, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.214 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.

Chennamadhavuni, D., Saavedra-Avila, N.A., Carreno, L.J., Guberman-Pfeffer, M.J., Arora, P., Yongqing, T., Koay, H.F., Godfrey, D.I., Keshipeddy, S., Richardson, S.K., Sundararaj, S., Lo, J.H., Wen, X., Gascon, J.A., Yuan, W., Rossjohn, J., Le Nours, J., Porcelli, S.A., Howell, A.R.

(2018) Cell Chem Biol 25: 571

• PubMed: 29576533 
• DOI: 10.1016/j.chembiol.2018.02.009
• Primary Citation of Related Structures:  
  6BNK, 6BNL


• PubMed Abstract: 
  

Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine variants of α-galactosylceramide as promising iNKT cell activators that stimulate cytokine responses with a strongly proinflammatory bias. However, the activities of sphinganine variants in mice have generally not translated well to studies of human iNKT cell responses. Here, we show that strongly proinflammatory and anti-tumor iNKT cell responses were achieved in mice by a variant of α-galactosylceramide that combines a sphinganine base with a hydrocinnamoyl ester on C6″ of the sugar. Importantly, the activities observed with this variant were largely preserved for human iNKT cell responses. Structural and in silico modeling studies provided a mechanistic basis for these findings and suggested basic principles for capturing useful properties of sphinganine analogs of synthetic iNKT cell activators in the design of immunotherapeutic agents.

---

Organizational Affiliation: 

Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A, E	302	Mus musculus	Mutation(s): 0  Gene Names: Cd1d1, mCG_3074, Cd1.1
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, F	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains	C, G	207	Homo sapiens	Mutation(s): 0  Gene Names: B2M, HDCMA22P

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains	D, H	242	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)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QWV	M [auth A], P [auth E]	N-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide C59 H107 N O9 ROLREGVMOYCGJS-XRHAFTOMSA-N
NAG	K [auth A], L [auth A], N [auth E], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.214 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.666	α = 90
b = 150.318	β = 96.12
c = 100.144	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-11-16 
• Released Date: 2018-04-04 
Deposition Author(s): Le Nours, J., Rossjohn, J.

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Data collection, Database references
• Version 1.2: 2018-05-30
  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