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 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.

Macromolecule Content

• Total Structure Weight: 193.13 kDa 
• Atom Count: 12264 
• Modelled Residue Count: 1554 
• Deposited Residue Count: 1668 
• Unique protein chains: 4

3TVM

Structure of the mouse CD1d-SMC124-iNKT TCR complex

• PDB DOI: 10.2210/pdb3TVM/pdb

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


• Deposited: 2011-09-20 Released: 2012-02-01 
• Deposition Author(s): Girardi, E., Li, Y., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Glycolipids that Elicit IFN-gama-Biased Responses from Natural Killer T Cells

Tyznik, A.J., Farber, E., Girardi, E., Birkholz, A., Li, Y., Chitale, S., So, R., Arora, P., Khurana, A., Wang, J., Porcelli, S.A., Zajonc, D.M., Kronenberg, M., Howell, A.R.

(2011) Chem Biol 18: 1620-1630

• PubMed: 22195564 
• DOI: 10.1016/j.chembiol.2011.10.015
• Primary Citation of Related Structures:  
  3TVM


• PubMed Abstract: 
  

Natural killer T (NKT) cells recognize glycolipids presented by CD1d. The first antigen described, α-galactosyl ceramide (αGalCer), is a potential anticancer agent whose activity depends upon IFN-γ secretion. We report two analogs of αGalCer based on a naturally occurring glycosphingolipid, plakoside A. These compounds induce enhanced IFN-γ that correlates with detergent-resistant binding to CD1d and an increased stability of the lipid-CD1d complexes on antigen-presenting cells. Structural analysis on one of the analogs indicates that it is more deeply bound inside the CD1d groove, suggesting tighter lipid-CD1d interactions. To our knowledge, this is the first example in which structural information provides an explanation for the increased lipid-CD1d stability, likely responsible for the Th1 bias. We provide insights into the mechanism of IFN-γ-inducing compounds, and because our compounds activate human NKT cells, they could have therapeutic utility.

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Organizational Affiliation: 

Division of Developmental Immunology, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A, E	285	Mus musculus	Mutation(s): 1  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, F	99	Mus musculus	Mutation(s): 1  Gene Names: beta-2-microglobulin, 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 (mouse variable domain, human constant domain)	C, G	209	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Valpha14 (mouse variable domain, human constant domain)
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 (mouse variable domain, human constant domain)	D, H	241	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Vbeta8.2 (mouse variable domain, human constant domain)
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	I, K	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	J, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
07P	N [auth A], Q [auth E]	N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide C55 H107 N O8 BCHXWZQXEKOXKQ-IYKQKVLOSA-N
NAG	M [auth A], P [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	R [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.97	α = 90
b = 150.57	β = 96.35
c = 101.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-20 
• Released Date: 2012-02-01 
Deposition Author(s): Girardi, E., Li, Y., Zajonc, D.M.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary