4Y16

Crystal structure of the mCD1d/NC-aGC/iNKTCR ternary complex

PDB DOI: https://doi.org/10.2210/pdb4Y16/pdb

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

Deposited: 2015-02-06 Released: 2015-06-03
Deposition Author(s): Zajonc, D.M., Nemcovic, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.244
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 96.62 kDa
Atom Count: 6,527
Modelled Residue Count: 807
Deposited Residue Count: 834
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11609
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P01848A0A0B4J1J9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric TCR Vbeta8.2 chain (mouse variable domain, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A0A5B9A2NTY6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
48G Query on 48G Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	N-[(2S,3S,4R)-3,4-dihydroxy-1-{[6-O-(naphthalen-1-ylcarbamoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide C₆₁ H₁₀₆ N₂ O₁₀ FWXGYYGDUQYCLV-DBQLOCGYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.244
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.64	α = 90
b = 191.914	β = 90
c = 151.92	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-03

Deposition Author(s):

Zajonc, D.M.

Nemcovic, M.

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

Revision History (Full details and data files)

Version 1.0: 2015-06-03
Type: Initial release
Version 1.1: 2015-06-10
Changes: Database references
Version 1.2: 2015-07-22
Changes: Database references
Version 1.3: 2016-07-27
Changes: Data collection
Version 1.4: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 1.5: 2017-11-22
Changes: Refinement description
Version 1.6: 2019-12-11
Changes: Author supporting evidence
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