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6XQP

Non-classical MHC Class I molecule MR1 with Alpha/Beta T cell receptor at 2.90Å 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

Mr1 with alpha beta tcr

1. Beta 2 microglobulin
['B', 'D']
2. MR1
['A', 'C']
3. T cell receptor alpha
TRAV12
['E']
4. T cell receptor beta
TRBV29
['F']

Species

Locus / Allele group

Non-classical MHC Class I molecule

Publication

Atypical TRAV1-2- T cell receptor recognition of the antigen-presenting molecule MR1.

Awad W, Meermeier EW, Sandoval-Romero ML, Le Nours J, Worley AH, Null MD, Liu L, McCluskey J, Fairlie DP, Lewinsohn DM, Rossjohn J
J. Biol. Chem. (2020) [doi:10.1074/jbc.RA120.015292]  [pubmed:32817339] 

MR1 presents vitamin B-related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2+ αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2- MR1-restricted T cell repertoire exists that can possess altered specificity for MR1 antigens. However, the molecular basis of how such TRAV1-2- TCRs interact with MR1-antigen complexes remains unclear. Here, we describe how a TRAV12-2+ TCR (termed D462-E4) recognizes an MR1-antigen complex. We report the crystal structures of the unliganded D462-E4 TCR and its complex with MR1 presenting the riboflavin-based antigen 5-OP-RU. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F'-pocket of MR1, whereby the complementarity-determining region (CDR) 3β loop surrounded and projected into the F'-pocket. Nevertheless, the CDR3β loop anchored proximal to the MR1 A'-pocket and mediated direct contact with the 5-OP-RU antigen. The D462-E4 TCR footprint on MR1 contrasted that of the TRAV1-2+ and TRAV36+ TCRs' docking topologies on MR1. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities.

Structure deposition and release

Deposited: 2020-07-10
Released: 2020-08-26
Revised: 2020-10-28

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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. MR1
MR1
        10        20        30        40        50        60
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
        70        80        90       100       110       120
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
       130       140       150       160       170       180
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
       190       200       210       220       230       240
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
       250       260       270
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP
3. T cell receptor alpha
T cell receptor alpha
TRAV12
        10        20        30        40        50        60
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDG
        70        80        90       100       110       120
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVRDAGNMLTFGGGTRLMVKPNIQNPDPAV
       130       140       150       160       170       180
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
       190       200
DFACANAFNNSIIPEDTFFPSPESS
4. T cell receptor beta
T cell receptor beta
TRBV29
        10        20        30        40        50        60
MSAVISQKPSRDICQRGTSLTIQCQVDSQVTMMFWYRQQPGQSLTLIATANQGSEATYES
        70        80        90       100       110       120
GFVIDKFPISRPNLTFSTLTVSNMSPEDSSIYLCSVGGDSLIGNQPQHFGDGTRLSILED
       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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Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 6XQP assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6XQP assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6XQP assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6xqp

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.