1YPZ

Mouse Non-classical MHC Class I molecule H2-T22 with Gamma/Delta T cell receptor at 3.40Å 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.

Complex type

H2 22 with gamma delta tcr

1. Beta 2 microglobulin

['B', 'D']

2. H2-T22

['A', 'C']

3. T cell receptor delta
TRDV10

['E']

4. T cell receptor gamma
TRGV4

['F']

Information on this structure on STCRdab.

Species

Mus musculus (Mouse)

Locus / Allele group

Non-classical MHC Class I molecule

Publication

Structure of a gammadelta T cell receptor in complex with the nonclassical MHC T22.

Adams EJ, Chien YH, Garcia KC

Science (2005) 308, 227-31 [doi:10.1126/science.1106885] [pubmed:15821084]

Gammadelta T cell receptors (TCRs), alphabeta TCRs, and antibodies are the three lineages of somatically recombined antigen receptors. The structural basis for ligand recognition is well defined for alphabeta TCR and antibodies but is lacking for gammadelta TCRs. We present the 3.4 A structure of the murine gammadelta TCR G8 bound to its major histocompatibility complex (MHC) class Ib ligand, T22. G8 predominantly uses germline-encoded residues of its delta chain complementarity-determining region 3 (CDR3) loop to bind T22 in an orientation substantially different from that seen in alphabeta TCR/peptide-MHC. That junctionally encoded G8 residues play an ancillary role in binding suggests a fusion of innate and adaptive recognition strategies.

Structure deposition and release

Deposited: 2005-01-31

Released: 2005-04-12

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 ADPIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS 70 80 90 100 KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. H2-T22 H2-T22	10 20 30 40 50 60 GSHSLRYFYTAVSRPGLGEPWFIIVGYVDDMQVLRFSSKEETPRMAPWLEQEEADNWEQQ 70 80 90 100 110 120 TRIVTIQGQLSERNLMTLVHFYNKSMDDSHTLQWLQGCDVEPDRHLCLWYNQLAYDSEDL 130 140 150 160 170 180 PTLNENPSSCTVGNSTVPHISQDLKSHCSDLLQKYLEKGKERLLRSDPPKAHVTRHPRPE 190 200 210 220 230 240 GDVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWAAVVVPLGKEQS 250 YTCHVYHEGLPEPLILRWGG

3. T cell receptor delta T cell receptor delta TRDV10	10 20 30 40 50 60 GDQVEQSPSALSLHEGTDSALRCNFTTTMRSVQWFRQNSRGSLISLFYLASGTKENGRLK 70 80 90 100 110 120 SAFDSKERRYSTLHIRDAQLEDSGTYFCAADTWHISEGYELGTDKLVFGQGTQVTVEPKS 130 140 150 160 170 180 QPPAKPSVFIMKNGTNVACLVKDFYPKEVTISLRSSKKIVEFDPAIVISPSGKYSAVKLG 190 200 QYGDSNSVTCSVQHNSETVHSTDFEAA

4. T cell receptor gamma T cell receptor gamma TRGV4	10 20 30 40 50 60 HGKLEQPEISISRPRDETAQISCKVFIESFRSVTIHWYRQKPNQGLEFLLYVLATPTHIF 70 80 90 100 110 120 LDKEYKKMEASKNPSASTSILTIYSLEEEDEAIYYCSYGEGSSGFHKVFAEGTKLIVIPS 130 140 150 160 170 180 DKRLDADISPKPTIFLPSVAETNLHKTGTYLCLLEAFFPDVIRVYWKEKDGNTILDSQEG 190 200 210 220 DTLKTNDTYMKFSWLTVPERAMGKEHRCIVKHENNKGGADQAIFFPSIKK

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]

1YPZ assembly 1

Components

MHC Class I alpha chain [cif]

1YPZ assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

1YPZ assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/1ypz

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.

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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

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