Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 2.80Å resolution
Data provenance
Information sections
Complex type
TRAV11
TRBV13
Species
Locus / Allele group
Structural and functional characterization of a novel nonglycosidic type I NKT agonist with immunomodulatory properties.
Activation of type I NKT (iNKT) cells by CD1d-presented agonists is a potent immunotherapeutic tool. α-Galactosylceramide (α-GalCer) is the prototypic agonist, but its excessive potency with simultaneous production of both pro- and anti-inflammatory cytokines hampers its potential therapeutic use. In search for novel agonists, we have analyzed the structure and function of HS44, a synthetic aminocyclitolic ceramide analog designed to avoid unrestrained iNKT cell activation. HS44 is a weaker agonist compared with α-GalCer in vitro, although in vivo it induces robust IFN-γ production, and highly reduced but still functional Th2 response. The characteristic cytokine storm produced upon α-GalCer activation was not induced. Consequently, HS44 induced a very efficient iNKT cell-dependent antitumoral response in B16 animal model. In addition, intranasal administration showed the capacity to induce lung inflammation and airway hyperreactivity, a cardinal asthma feature. Thus, HS44 is able to elicit functional Th1 or Th2 responses. Structural studies show that HS44 binds to CD1d with the same conformation as α-GalCer. The TCR binds to HS44 similarly as α-GalCer, but forms less contacts, thus explaining its weaker TCR affinity and, consequently, its weaker recognition by iNKT cells. The ability of this compound to activate an efficient, but not massive, tailored functional immune response makes it an attractive reagent for immune manipulation.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW 70 80 90 SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM |
2. CD1d
CD1d
|
10 20 30 40 50 60
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN 70 80 90 100 110 120 QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF 130 140 150 160 170 180 QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK 190 200 210 220 230 240 SDLEKQEKPVAWLSSVPSSADGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN 250 260 270 280 ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH |
3. T cell receptor alpha
T cell receptor alpha
TRAV11
|
10 20 30 40 50 60
MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSN 70 80 90 100 110 120 GRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNP 130 140 150 160 170 180 DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW 190 200 SNKSDFACANAFNNSIIPEDTFFPSPESS |
4. T cell receptor beta
T cell receptor beta
TRBV13
|
10 20 30 40 50 60
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD 70 80 90 100 110 120 IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTP 130 140 150 160 170 180 PKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA 190 200 210 220 230 240 LNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR A |
Data provenance
Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.
Downloadable data
Components
Data license
Footnotes
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint

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