4ELK

Crystal structure of the Hy19.3 type II NKT TCR

PDB DOI: https://doi.org/10.2210/pdb4ELK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-04-10 Released: 2012-07-25
Deposition Author(s): Girardi, E., Maricic, I., Wang, J., Mac, T.T., Iyer, P., Kumar, V., Zajonc, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.227
R-Value Work: 0.188
R-Value Observed: 0.190

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.

Girardi, E., Maricic, I., Wang, J., Mac, T.T., Iyer, P., Kumar, V., Zajonc, D.M.

(2012) Nat Immunol 13: 851-856

PubMed: 22820602 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ni.2371
Primary Citation of Related Structures:
4ELK, 4ELM

PubMed Abstract:
Glycolipids presented by the major histocompatibility complex (MHC) class I homolog CD1d are recognized by natural killer T cells (NKT cells) characterized by either a semi-invariant T cell antigen receptor (TCR) repertoire (type I NKT cells or iNKT cells) or a relatively variable TCR repertoire (type II NKT cells). Here we describe the structure of a type II NKT cell TCR in complex with CD1d-lysosulfatide. Both TCR α-chains and TCR β-chains made contact with the CD1d molecule with a diagonal footprint, typical of MHC-TCR interactions, whereas the antigen was recognized exclusively with a single TCR chain, similar to the iNKT cell TCR. Type II NKT cell TCRs, therefore, recognize CD1d-sulfatide complexes by a distinct recognition mechanism characterized by the TCR-binding features of both iNKT cells and conventional peptide-reactive T cells.

Organizational Affiliation

Division of Cell Biology, La Jolla Institute for Allergy & Immunology, La Jolla, California, USA.

Macromolecule Content

Total Structure Weight: 103.13 kDa
Atom Count: 7,309
Modelled Residue Count: 886
Deposited Residue Count: 904
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)	A, C	208	Mus musculus	Mutation(s): 0 Gene Names: Valpha1 (mouse variable domain, human constant domain)
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hy19.3 TCR beta chain (mouse variable domain, human constant domain)	B, D	244	Mus musculus	Mutation(s): 0 Gene Names: Vbeta16 (mouse variable domain, human constant domain)
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], F [auth A], H [auth A], J [auth B], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D]	G [auth A] L [auth B] M [auth B] N [auth B] O [auth C] G [auth A], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.227
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 73.22	α = 90
b = 101.53	β = 90
c = 134.49	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-25
Type: Initial release
Version 1.1: 2013-01-09
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4ELK

Crystal structure of the Hy19.3 type II NKT TCR

Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2