Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 3.20Å resolution
Data provenance
Information sections
Complex type
TRAV11
TRBV13
Species
Locus / Allele group
Dual Modifications of ��-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.
Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine variants of α-galactosylceramide as promising iNKT cell activators that stimulate cytokine responses with a strongly proinflammatory bias. However, the activities of sphinganine variants in mice have generally not translated well to studies of human iNKT cell responses. Here, we show that strongly proinflammatory and anti-tumor iNKT cell responses were achieved in mice by a variant of α-galactosylceramide that combines a sphinganine base with a hydrocinnamoyl ester on C6″ of the sugar. Importantly, the activities observed with this variant were largely preserved for human iNKT cell responses. Structural and in silico modeling studies provided a mechanistic basis for these findings and suggested basic principles for capturing useful properties of sphinganine analogs of synthetic iNKT cell activators in the design of immunotherapeutic agents.
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 SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN 250 260 270 280 290 300 ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH HH |
3. T cell receptor alpha
T cell receptor alpha
TRAV11
|
10 20 30 40 50 60
TQVEQSPQSLVVRQGENSVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGR 70 80 90 100 110 120 YSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDP 130 140 150 160 170 180 AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN 190 200 KSDFACANAFNNSIIPEDTFFPSPESS |
4. T cell receptor beta
T cell receptor beta
TRBV13
|
10 20 30 40 50 60
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD 70 80 90 100 110 120 IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLKNVFP 130 140 150 160 170 180 PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA 190 200 210 220 230 240 LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR AD |
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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