6OMG | pdb_00006omg

Structure of mouse CD1D- Glc-DAG (sn-1 C18:0, sn-2 C18:1c9)-iNKT TCR Ternary complex

PDB DOI: https://doi.org/10.2210/pdb6OMG/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-04-18 Released: 2020-04-22
Deposition Author(s): Dirk, M.Z., Bitra, A., Wang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.227 (Depositor), 0.236 (DCC)
R-Value Work:
0.186 (Depositor), 0.195 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structure of mouse CD1D- Glc-DAG (sn-1 C18:0, sn-2 C18:1c9)-iNKT TCR Ternary complex

Dirk, M.Z., Bitra, A., Wang, J.

To be published.

Macromolecule Content

Total Structure Weight: 97.06 kDa
Atom Count: 7,015
Modeled Residue Count: 811
Deposited Residue Count: 834
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIMERIC T CELL ANTIGEN RECEPTOR ALPHA CHAIN VA14,VA24	A [auth C]	209	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIMERIC T CELL ANTIGEN RECEPTOR BETA CHAIN VB8.2, VB11	B [auth D]	241	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	C [auth A]	285	Mus musculus	Mutation(s): 0 Gene Names: Cd1d1, mCG_3074
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11609
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C [auth A]	Go to GlyGen: P11609-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [auth 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MVV Query on MVV Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	(2R)-1-(alpha-D-glucopyranosyloxy)-3-(octadecanoyloxy)propan-2-yl (9Z)-octadec-9-enoate C₄₅ H₈₄ O₁₀ STIYDDOYHOERHV-JTDQAXPSSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	H [auth C], I [auth C], L [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain L [auth A] Focus chain M [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain K [auth D] SDF format, chain J [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C]	J [auth C], K [auth D], O [auth A], P [auth A], Q [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain J [auth C] Focus chain K [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.227 (Depositor), 0.236 (DCC)
R-Value Work: 0.186 (Depositor), 0.195 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.692	α = 90
b = 191.25	β = 90
c = 151.29	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Dirk, M.Z.

Bitra, A.

Wang, J.

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary