3ARD

Ternary crystal structure of the mouse NKT TCR-CD1d-3'deoxy-alpha-galactosylceramide

• PDB DOI: https://doi.org/10.2210/pdb3ARD/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: 3.01 Å
• R-Value Free: 0.277 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.37 kDa 
• Atom Count: 6,466 
• Modelled Residue Count: 833 
• Deposited Residue Count: 852 
• Unique protein chains: 4

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 & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609
IMPC:  MGI:107674

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	Length	2D Diagram	Glycosylation	3D Interactions
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
3GH	H [auth A]	N-{(2S,3R)-1-[(3-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide C50 H99 N O7 XFTWWKOPEFGPIP-AYIWZJAFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3GH	PDBBind:  3ARD	Kd: 175 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.277 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.991	α = 90
b = 86.732	β = 90
c = 235.198	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary