6MJ4

Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW)

PDB DOI: https://doi.org/10.2210/pdb6MJ4/pdb

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

Deposited: 2018-09-20 Released: 2019-01-09
Deposition Author(s): Zajonc, D.M., Bitra, A., Janssens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.185
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 97.07 kDa
Atom Count: 7,315
Modelled Residue Count: 811
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
T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein	A [auth C]	209	Mus musculus, Homo sapiens	Mutation(s): 0 Gene Names: Trav11, Trav11d, Traj18, B2M, HDCMA22P
UniProt
Find proteins for A0A0B4J1J9 (Mus musculus) Explore A0A0B4J1J9 Go to UniProtKB: A0A0B4J1J9
Find proteins for K7N5M3 (Homo sapiens) Explore K7N5M3 Go to UniProtKB: K7N5M3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	K7N5M3A0A0B4J1J9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN	B [auth D]	241	Mus musculus, Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for A0N8J3 (Mus musculus) Explore A0N8J3 Go to UniProtKB: A0N8J3
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	A0N8J3A0A5B9A2NTY6
Sequence Annotations Expand
Reference Sequence

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

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01887
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)-[alpha-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: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JTG Query on JTG Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	N-[(2S,3S,4R)-3,4-dihydroxy-1-{[4-O-(prop-2-en-1-yl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide C₅₃ H₁₀₃ N O₉ ALFONRPZUQLTFA-BDHLTHOMSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-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 G [auth C] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	G [auth C] H [auth C] I [auth C] J [auth C] L [auth A] G [auth C], H [auth C], I [auth C], J [auth C], L [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth A] Focus chain M [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D]	K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.185
R-Value Observed: 0.186
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.948	α = 90
b = 190.723	β = 90
c = 151.145	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-09

Deposition Author(s):

Zajonc, D.M.

Bitra, A.

Janssens, J.

Revision History (Full details and data files)

Version 1.0: 2019-01-09
Type: Initial release
Version 1.1: 2019-01-16
Changes: Data collection, Database references
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