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.

Macromolecule Content

• Total Structure Weight: 98.55 kDa 
• Atom Count: 6647 
• Modelled Residue Count: 816 
• Deposited Residue Count: 853 
• Unique protein chains: 4

3SDD

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide

• DOI: 10.2210/pdb3SDD/pdb

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


• Deposited: 2011-06-09 Released: 2011-10-05 
• Deposition Author(s): Clarke, A.J., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.318 
• R-Value Work: 0.258 
• R-Value Observed: 0.261 

Literature

Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors

Pellicci, D.G., Clarke, A.J., Patel, O., Mallevaey, T., Beddoe, T., Le Nours, J., Uldrich, A.P., McCluskey, J., Besra, G.S., Porcelli, S.A., Gapin, L., Godfrey, D.I., Rossjohn, J.

(2011) Nat Immunol 12: 827-833

• PubMed: 21804559 
• DOI: 10.1038/ni.2076
• Primary Citation of Related Structures:  
  3SCM, 3SDA, 3SDC, 3SDD, 3SDX


• PubMed Abstract: 
  

The most potent foreign antigens for natural killer T cells (NKT cells) are α-linked glycolipids, whereas NKT cell self-reactivity involves weaker recognition of structurally distinct β-linked glycolipid antigens. Here we provide the mechanism for the autoreactivity of T cell antigen receptors (TCRs) on NKT cells to the mono- and tri-glycosylated β-linked agonists β-galactosylceramide (β-GalCer) and isoglobotrihexosylceramide (iGb3), respectively. In binding these disparate antigens, the NKT cell TCRs docked onto CD1d similarly, achieving this by flattening the conformation of the β-linked ligands regardless of the size of the glycosyl head group. Unexpectedly, the antigenicity of iGb3 was attributable to its terminal sugar group making compensatory interactions with CD1d. Thus, the NKT cell TCR molds the β-linked self ligands to resemble the conformation of foreign α-linked ligands, which shows that induced-fit molecular mimicry can underpin the self-reactivity of NKT cell TCRs to β-linked antigens.

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Organizational Affiliation: 

Department of Microbiology & Immunology, University of Melbourne, Parkville, Victoria, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	302	Mus musculus	Mutation(s): 0  Gene Names: Cd1.1, 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
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 TCR Valpha14 chain	C	207	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NKT TCR autoreactive-Vbeta6 chain	D	245	Mus musculus, Homo sapiens This entity is chimeric	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	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3GD (Subject of Investigation/LOI)	H [auth A]	N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide C52 H99 N O13 QYWVASPEUXEHSY-NNRNTGNWSA-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

Binding Affinity Annotations
ID	Source	Binding Affinity
3GD	PDBBind:  3SDD	Kd: 4840 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.318 
• R-Value Work: 0.258 
• R-Value Observed: 0.261 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.469	α = 90
b = 94.469	β = 90
c = 291.063	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2011-06-09 
• Released Date: 2011-10-05 
Deposition Author(s): Clarke, A.J., Rossjohn, J.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary