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6D7G

Single chain construct of HLA-A*02:01 presenting "None" to Gamma/Delta T cell receptor at 2.75Å 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

Single chain class i construct with gamma delta tcr

1. Class I alpha
HLA-A*02:01
['A']
2. T cell receptor delta
TRDV1
['D']
3. T cell receptor gamma
TRGV8
['E']

Species


Locus / Allele group


Publication

Generation and molecular recognition of melanoma-associated antigen-specific human ���� T cells.

Benveniste PM, Roy S, Nakatsugawa M, Chen ELY, Nguyen L, Millar DG, Ohashi PS, Hirano N, Adams EJ, Z����iga-Pfl��cker JC
Sci Immunol (2018) 3, [doi:10.1126/sciimmunol.aav4036]  [pubmed:30552102

Antigen recognition by T cells bearing αβ T cell receptors (TCRs) is restricted by major histocompatibility complex (MHC). However, how antigens are recognized by T cells bearing γδ TCRs remains unclear. Although γδ T cells can recognize nonclassical MHC, it is generally thought that recognition of antigens is not MHC restricted. Here, we took advantage of an in vitro system to generate antigen-specific human T cells and show that melanoma-associated antigens, MART-1 and gp100, can be recognized by γδ T cells in an MHC-restricted fashion. Cloning and transferring of MART-1-specific γδ TCRs restored the specific recognition of the initial antigen MHC/peptide reactivity and conferred antigen-specific functional responses. A crystal structure of a MART-1-specific γδ TCR, together with MHC/peptide, revealed distinctive but similar docking properties to those previously reported for αβ TCRs, recognizing MART-1 on HLA-A*0201. Our work shows that antigen-specific and MHC-restricted γδ T cells can be generated in vitro and that MART-1-specific γδ T cells can also be found and cloned from the naïve repertoire. These findings reveal that classical MHC-restricted human γδ TCRs exist in the periphery and have the potential to be used in developing of new TCR-based immunotherapeutic approaches.

Structure deposition and release

Deposited: 2018-04-24
Released: 2019-01-23
Revised: 2020-07-29

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

PRO159
GLU163
ILE167
TYR171
ILE5
ASP59
ASP63
LYS66
ILE7
B Pocket

GLY24
VAL34
SER45
ASP63
LYS66
ASN67
ILE7
ARG70
THR9
GLU99
C Pocket

ARG70
LYS73
VAL74
THR9
PRO97
D Pocket

GLN114
SER155
VAL156
PRO159
GLY160
GLU99
E Pocket

GLN114
HIS147
PHE152
VAL156
PRO97
F Pocket

LYS116
ASP123
GLY143
SER146
HIS147
SER77
SER80
PHE81
ASP84
PHE95

Colour key

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

1. Class I alpha
HLA-A*02:01
IPD-IMGT/HLA
[ipd-imgt:HLA35266]
        10        20        30        40        50        60
ELAGIGILTVGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDI
        70        80        90       100       110       120
EVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKW
       130       140       150       160       170       180
DRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
       190       200       210       220       230       240
DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQ
       250       260       270       280       290       300
RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL
       310       320       330       340       350       360
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
       370       380       390       400       410       420
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEH

HHHHHHH

2. T cell receptor delta
T cell receptor delta
TRDV1
        10        20        30        40        50        60
ADPAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQN
        70        80        90       100       110       120
AKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGELGWDTDKLIFGKGTRVTVEPRS
       130       140       150       160       170       180
QPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLG
       190       200       210       220
KYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENTKQPSKSC

3. T cell receptor gamma
T cell receptor gamma
TRGV8
        10        20        30        40        50        60
ADLSSNLEGRTKSVTRPTGSSAVITCDLPVENAVYTHWYLHQEGKAPQRLLYYDSYNSRV
        70        80        90       100       110       120
VLESGISREKYHTYASTGKSLKFILENLIERDSGVYYCATWASSDWIKTFAKGTRLIVTS
       130       140       150       160       170       180
PDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDIIKIHWQEKKSNTILGSQE
       190       200       210       220       230       240
GNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGIDQEIIFPPIKTDVTTVDPKY
       250
NYSKDANDVITMDPKDNC


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. 6D7G assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6D7G assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6D7G assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6d7g

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