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6MWR

Non-classical MHC Class I molecule MR1 with Gamma/Delta T cell receptor at 3.30Å 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 gamma delta tcr

1. Beta 2 microglobulin
['B']
2. MR1
['A']
3. T cell receptor delta
TRDV1
['D']
4. T cell receptor gamma
TRGV9
['C']

Species

Locus / Allele group

Non-classical MHC Class I molecule

Publication

A class of ���� T cell receptors recognize the underside of the antigen-presenting molecule MR1.

Le Nours J, Gherardin NA, Ramarathinam SH, Awad W, Wiede F, Gully BS, Khandokar Y, Praveena T, Wubben JM, Sandow JJ, Webb AI, von Borstel A, Rice MT, Redmond SJ, Seneviratna R, Sandoval-Romero ML, Li S, Souter MNT, Eckle SBG, Corbett AJ, Reid HH, Liu L, Fairlie DP, Giles EM, Westall GP, Tothill RW, Davey MS, Berry R, Tiganis T, McCluskey J, Pellicci DG, Purcell AW, Uldrich AP, Godfrey DI, Rossjohn J
Science (2019) 366, 1522-1527 [doi:10.1126/science.aav3900]  [pubmed:31857486] 

T cell receptors (TCRs) recognize antigens presented by major histocompatibility complex (MHC) and MHC class I-like molecules. We describe a diverse population of human γδ T cells isolated from peripheral blood and tissues that exhibit autoreactivity to the monomorphic MHC-related protein 1 (MR1). The crystal structure of a γδTCR-MR1-antigen complex starkly contrasts with all other TCR-MHC and TCR-MHC-I-like complex structures. Namely, the γδTCR binds underneath the MR1 antigen-binding cleft, where contacts are dominated by the MR1 α3 domain. A similar pattern of reactivity was observed for diverse MR1-restricted γδTCRs from multiple individuals. Accordingly, we simultaneously report MR1 as a ligand for human γδ T cells and redefine the parameters for TCR recognition.

Structure deposition and release

Deposited: 2018-10-30
Released: 2019-12-18
Revised: 2020-07-29

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
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
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 delta
T cell receptor delta
TRDV1
        10        20        30        40        50        60
AQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKS
        70        80        90       100       110       120
GRYSVNFKKAAKSVALTISALQLEDSAKYFCALGVRAFLRDWGIRVLIFGKGTRVTVEPR
       130       140       150       160       170       180
SQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKL
       190       200       210       220       230
GKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENTKQPSKSASGLVPR
4. T cell receptor gamma
T cell receptor gamma
TRGV9
        10        20        30        40        50        60
AGHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRK
        70        80        90       100       110       120
ESGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWDRYYKKLFGSGTTLVVTDKQ
       130       140       150       160       170       180
LDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTM
       190       200       210       220       230       240
KTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMDPKDNASG

LVPR

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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or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
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. 6MWR assembly 1  

Components

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

Derived data

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

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.