4Y4K

Crystal structure of the mCD1d/EF77/iNKTCR ternary complex

• PDB DOI: https://doi.org/10.2210/pdb4Y4K/pdb

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


• Deposited: 2015-02-10 Released: 2015-05-27 
• Deposition Author(s): Zajonc, D.M., Birkholz, A.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.19 kDa 
• Atom Count: 6,308 
• Modelled Residue Count: 805 
• 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): 1  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
chimeric TCR Valpha14Jalpha18 chain (mouse variable, human constant domain)	C	209	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Trav11, Trav11d
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848
Find proteins for A0A0B4J1J9 (Mus musculus) Explore A0A0B4J1J9  Go to UniProtKB:  A0A0B4J1J9
UniProt Groups	P01848A0A0B4J1J9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
chimeric TCR Vbeta8.2 chain (mouse variable, human constant domain)	D	241	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: TRBC2, TCRBC2
UniProt & NIH Common Fund Data Resources
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6  Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9  Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9
UniProt Groups	A0A5B9A2NTY6

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
49Y	H [auth A]	(4Z)-9-[(1R,2R)-2-decylcyclopropyl]-N-[(2S,3S,4S)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]non-4-enamide C46 H87 N O9 MUTIAULHGSSWRA-AHDGLNOFSA-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: 2.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.96	α = 90
b = 191.07	β = 90
c = 151.08	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Zajonc, D.M., Birkholz, A.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI074952

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Data collection
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary