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: 98.31 kDa 
• Atom Count: 6501 
• Modelled Residue Count: 830 
• Deposited Residue Count: 852 
• Unique protein chains: 4

3ARF

Ternary crystal structure of the mouse NKT TCR-CD1d-C20:2

• DOI: 10.2210/pdb3ARF/pdb

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


• Deposited: 2010-11-27 Released: 2011-03-30 
• Deposition Author(s): Wun, K.S., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.277 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Literature

A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells

Wun, K.S., Cameron, G., Patel, O., Pang, S.S., Pellicci, D.G., Sullivan, L.C., Keshipeddy, S., Young, M.H., Uldrich, A.P., Thakur, M.S., Richardson, S.K., Howell, A.R., Illarionov, P.A., Brooks, A.G., Besra, G.S., McCluskey, J., Gapin, L., Porcelli, S.A., Godfrey, D.I., Rossjohn, J.

(2011) Immunity 34: 327-339

• PubMed: 21376639 
• DOI: 10.1016/j.immuni.2011.02.001
• Primary Citation of Related Structures:  
  3ARB, 3ARD, 3ARE, 3ARF, 3ARG


• PubMed Abstract: 
  

Natural killer T (NKT) cells respond to a variety of CD1d-restricted antigens (Ags), although the basis for Ag discrimination by the NKT cell receptor (TCR) is unclear. Here we have described NKT TCR fine specificity against several closely related Ags, termed altered glycolipid ligands (AGLs), which differentially stimulate NKT cells. The structures of five ternary complexes all revealed similar docking. Acyl chain modifications did not affect the interaction, but reduced NKT cell proliferation, indicating an affect on Ag processing or presentation. Conversely, truncation of the phytosphingosine chain caused an induced fit mode of TCR binding that affected TCR affinity. Modifications in the glycosyl head group had a direct impact on the TCR interaction and associated cellular response, with ligand potency reflecting the t(1/2) life of the interaction. Accordingly, we have provided a molecular basis for understanding how modifications in AGLs can result in striking alterations in the cellular response of NKT cells.

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Organizational Affiliation: 

The Protein Crystallography Unit, ARC Centre of Excellence in Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, 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: Cd1d1, 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	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-Jalpha18,NKT Valpha14-Jalpha18	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
Vbeta8.2,Vbeta8.2	D	244	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

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, F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DB3 (Subject of Investigation/LOI)	H [auth A]	(11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide C44 H83 N O9 WSXMIFGRYXQZQZ-HJCGRHBQSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DB3	PDBBind:  3ARF	Kd: 64 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.277 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.95	α = 90
b = 87.046	β = 90
c = 234.86	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2010-11-27 
• Released Date: 2011-03-30 
Deposition Author(s): Wun, K.S., Rossjohn, J.

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-29
  Changes: Database references
• Version 1.3: 2020-01-22
  Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary