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.

Macromolecule Content

• Total Structure Weight: 96.35 kDa 
• Atom Count: 6598 
• Modelled Residue Count: 813 
• Deposited Residue Count: 834 
• Unique protein chains: 4

3O9W

Recognition of a Glycolipid Antigen by the iNKT Cell TCR

• PDB DOI: 10.2210/pdb3O9W/pdb

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


• Deposited: 2010-08-04 Released: 2010-09-29 
• Deposition Author(s): Zajonc, D.M., Li, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

The V{alpha}14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.

Li, Y., Girardi, E., Wang, J., Yu, E.D., Painter, G.F., Kronenberg, M., Zajonc, D.M.

(2010) J Exp Med 

• PubMed: 20921281 
• DOI: 10.1084/jem.20101335
• Primary Citation of Related Structures:  
  3O8X, 3O9W


• PubMed Abstract: 
  

Invariant natural killer T cells (iNKT cells) rapidly produce effector cytokines. In this study, we report the first crystal structures of the iNKT cell T cell receptor (TCR) bound to two natural, microbial glycolipids presented by CD1d. Binding of the TCR induced CDR3-α-dependent structural changes in the F' roof of CD1d; these changes resemble those occurring in the absence of TCR engagement when the highly potent synthetic antigen α-galactosylceramide (α-GalCer) binds CD1d. Furthermore, in the Borrelia burgdorferi α-galactosyl diacylglycerol-CD1d complex, TCR binding caused a marked repositioning of the galactose sugar into an orientation that closely resembles α-GalCer. The TCR-dependent reorientation of the sugar, together with the induced CD1d fit, may explain the weaker potency of the microbial antigens compared with α-GalCer. We propose that the TCR of iNKT cells binds with a conserved footprint onto CD1d, regardless of the bound glycolipid antigen, and that for microbial antigens this unique binding mode requires TCR-initiated conformational changes.

---

Organizational Affiliation: 

Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

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
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
Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain)	C	209	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 1  Gene Names: TRAC, TCRA
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 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain)	D	241	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 2  Gene Names: TRBC2, TCRBC2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9  Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9

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

Entity ID: 6
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	F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1O2	H [auth A]	(2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate C43 H80 O10 JBZBYHKCRFIXBI-BNOJPGAFSA-N
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TCR	PDBBind:  3O9W	Kd: 6200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.003	α = 90
b = 188.368	β = 90
c = 149.791	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

Entry History 

Deposition Data

• Deposited Date: 2010-08-04 
• Released Date: 2010-09-29 
Deposition Author(s): Zajonc, D.M., Li, Y.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-06-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2017-06-28
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary