4IRJ

Structure of the mouse CD1d-4ClPhC-alpha-GalCer-iNKT TCR complex

• PDB DOI: https://doi.org/10.2210/pdb4IRJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-14 Released: 2013-08-28 
• Deposition Author(s): Nemcovic, M., Zajonc, D.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96.4 kDa 
• Atom Count: 6,381 
• Modelled Residue Count: 804 
• Deposited Residue Count: 834 
• Unique protein chains: 4

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 & 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, 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 (mouse variable domain, human constant domain)	C	209	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Valpha14 (mouse variable domain, human constant domain)

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

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1L9	H [auth A]	N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide C57 H103 Cl N2 O10 MAGJZLBUXUBUBN-FNBNLLHXSA-N
NAG	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.283	α = 90
b = 191.862	β = 90
c = 151.598	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Nemcovic, M., Zajonc, D.M.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2014-02-05
  Changes: Database references
• 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