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7RYM

Non-classical MHC Class I molecule CD1a with Natural Killer Gamma/Delta T cell receptor at 3.20Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Cd1a with nkt gamma delta tcr

1. Beta 2 microglobulin
['B']
2. CD1a
['A']
3. T cell receptor delta
TRDV1
['D']
4. T cell receptor gamma
TRGV4
['C']

Species


Locus / Allele group

Non-classical MHC Class I molecule

Publication

Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors.

Wegrecki, M., Ocampo, T.A., Gunasinghe, S.D., von Borstel, A., Tin, S.Y., Reijneveld, J.F., Cao, T.P., Gully, B.S., Le Nours, J., Moody, D.B., Van Rhijn, I., Rossjohn, J.
(2022) 13, 3872-3872 [doi:10.1038/s41467-022-31443-9]  [pubmed:35790773

CD1a is a monomorphic antigen-presenting molecule on dendritic cells that presents lipids to αβ T cells. Whether CD1a represents a ligand for other immune receptors remains unknown. Here we use CD1a tetramers to show that CD1a is a ligand for Vδ1+ γδ T cells. Functional studies suggest that two γδ T cell receptors (TCRs) bound CD1a in a lipid-independent manner. The crystal structures of three Vγ4Vδ1 TCR-CD1a-lipid complexes reveal that the γδ TCR binds at the extreme far side and parallel to the long axis of the β-sheet floor of CD1a's antigen-binding cleft. Here, the γδ TCR co-recognises the CD1a heavy chain and β2 microglobulin in a manner that is distinct from all other previously observed γδ TCR docking modalities. The 'sideways' and lipid antigen independent mode of autoreactive CD1a recognition induces TCR clustering on the cell surface and proximal T cell signalling as measured by CD3ζ phosphorylation. In contrast with the 'end to end' binding of αβ TCRs that typically contact carried antigens, autoreactive γδ TCRs support geometrically diverse approaches to CD1a, as well as antigen independent recognition.

Structure deposition and release

Deposited: 2021-08-25
Released: 2022-05-18
Revised: 2022-07-13

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
DAGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
        70        80        90       100
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

2. CD1a
CD1a
        10        20        30        40        50        60
DAATGLKEPLSFHVIWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNF
        70        80        90       100       110       120
SNEEWKELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAY
       130       140       150       160       170       180
QGSDFVSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGK
       190       200       210       220       230       240
AHLQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPS
       250       260       270       280
ADGTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWEGSLVPR

3. T cell receptor delta
T cell receptor delta
TRDV1
        10        20        30        40        50        60
MAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAK
        70        80        90       100       110       120
SGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGELRWPDKLIFGKGTRVTVEPNIQNP
       130       140       150       160       170       180
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
       190       200
SNKSDFACANAFNNSIIPEDTFFPSPESS

4. T cell receptor gamma
T cell receptor gamma
TRGV4
        10        20        30        40        50        60
MASSNLEGRTKSVIRQTGSSAEITCDLAEGSTGYIHWYLHQEGKAPQRLLYYDSYTSSVV
        70        80        90       100       110       120
LESGISPGKYDTYGSTRKNLRMILRNLIENDSGVYYCATWDGDYYKKLFGSGTTLVVTED
       130       140       150       160       170       180
LKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQP
       190       200       210       220       230       240
LKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVS

AEAWGRAD


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

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Complete structures

Aligned structures [cif]
  1. 7RYM assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7RYM assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7RYM assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7rym

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes