6MIY

Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex

PDB DOI: https://doi.org/10.2210/pdb6MIY/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: 2.75 Å
R-Value Free: 0.247
R-Value Work: 0.192
R-Value Observed: 0.194

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

Macromolecule Content

Total Structure Weight: 193.98 kDa
Atom Count: 13,394
Modelled Residue Count: 1,620
Deposited Residue Count: 1,668
Unique protein chains: 4

Macromolecules

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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], F [auth G]	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], G [auth H]	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], E	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
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [auth B], H [auth F]	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	I, J, L, N	2		N-Glycosylation	Interactions Focus chain I Focus chain J Focus chain L Focus chain N Interactions & Density Focus chain I Focus chain J Focus chain L Focus chain N
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	K, M	3		N-Glycosylation	Interactions Focus chain K Focus chain M Interactions & Density Focus chain K Focus chain M
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JTV Query on JTV Download Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain R [auth A] MOL2 format, chain U [auth E] MOL2 format, chain R [auth A]	R [auth A], U [auth E]	N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide C₅₇ H₁₀₅ N O₉ XDALVMZANJGPPV-VSVWWTSQSA-N		Interactions Focus chain R [auth A] Focus chain U [auth E] Interactions & Density Focus chain R [auth A] Focus chain U [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain V [auth E] SDF format, chain T [auth A] SDF format, chain W [auth G] MOL2 format, chain S [auth A] MOL2 format, chain V [auth E] MOL2 format, chain T [auth A] MOL2 format, chain W [auth G]	S [auth A], T [auth A], V [auth E], W [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth E] Focus chain W [auth G] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth E] Focus chain W [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D]	Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain X [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain X [auth G]	O [auth C], P [auth D], X [auth G], Y [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain P [auth D] Focus chain X [auth G] Focus chain Y [auth H] Interactions & Density Focus chain O [auth C] Focus chain P [auth D] Focus chain X [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.247
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.865	α = 90
b = 192.477	β = 90.79
c = 150.418	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

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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