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: 97.12 kDa 
• Atom Count: 6594 
• Modelled Residue Count: 807 
• Deposited Residue Count: 834 
• Unique protein chains: 4

3RZC

Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR

• PDB DOI: 10.2210/pdb3RZC/pdb

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


• Deposited: 2011-05-11 Released: 2011-08-24 
• Deposition Author(s): Yu, E.D., Girardi, E., Wang, J., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.271 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Literature

Cutting Edge: Structural Basis for the Recognition of {beta}-Linked Glycolipid Antigens by Invariant NKT Cells.

Yu, E.D., Girardi, E., Wang, J., Zajonc, D.M.

(2011) J Immunol 187: 2079-2083

• PubMed: 21810611 
• DOI: 10.4049/jimmunol.1101636
• Primary Citation of Related Structures:  
  3RZC


• PubMed Abstract: 
  

Invariant NKT (iNKT) cells expressing a semi-invariant Vα14 TCR recognize self and foreign lipid Ags when presented by the nonclassical MHCI homolog CD1d. Whereas the majority of known iNKT cell Ags are characterized by the presence of a single α-linked sugar, mammalian self Ags are β-linked glycosphingolipids, posing the interesting question of how the semi-invariant TCR can bind to such structurally distinct ligands. In this study, we show that the mouse iNKT TCR recognizes the complex β-linked Ag isoglobotrihexosylceramide (iGb3; Galα1-3-Galβ1-4-Glcβ1-1Cer) by forcing the proximal β-linked sugar of the trisaccharide head group to adopt the typical binding orientation of α-linked glycolipids. The squashed iGb3 orientation is stabilized by several interactions between the trisaccharide and CD1d residues. Finally, the formation of novel contacts between the proximal and second sugar of iGb3 and CDR2α residues of the TCR suggests an expanded recognition logic that can possibly distinguish foreign Ags from self Ags.

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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): 0  Gene Names: Cd1.1, CD1d, 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): 1  Gene Names: B2m, beta-2-microglobulin
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	C	209	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Valpha14

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vbeta8.2	D	241	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Vbeta8.2

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	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G70885YM GlyCosmos:  G70885YM GlyGen:  G70885YM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGN	H [auth A]	N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide C62 H117 N O18 JMENXJYBCQFIRK-KRJDXUSZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.271 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.103	α = 90
b = 191.346	β = 90
c = 151.032	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: 2011-05-11 
• Released Date: 2011-08-24 
Deposition Author(s): Yu, E.D., Girardi, E., Wang, J., Zajonc, D.M.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2011-09-07
  Changes: Database references
• Version 1.2: 2013-09-18
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary