5U16

Non-classical MHC Class I molecule MR1 with Alpha/Beta T cell receptor at 2.00Å 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

Mr1 with alpha beta tcr

1. Beta 2 microglobulin

['B', 'D']

2. MR1

['A', 'C']

3. T cell receptor alpha
TRAV1

['E']

4. T cell receptor beta
TRBV6

['F']

Information on this structure on STCRdab.

Species

Homo sapiens (Human)

Locus / Allele group

Non-classical MHC Class I molecule

Publication

Drugs and drug-like molecules can modulate the function of mucosal-associated invariant T cells.

Keller AN, Eckle SB, Xu W, Liu L, Hughes VA, Mak JY, Meehan BS, Pediongco T, Birkinshaw RW, Chen Z, Wang H, D'Souza C, Kjer-Nielsen L, Gherardin NA, Godfrey DI, Kostenko L, Corbett AJ, Purcell AW, Fairlie DP, McCluskey J, Rossjohn J

Nat. Immunol. (2017) [doi:10.1038/ni.3679] [pubmed:28166217]

L1₀-ordered FeNi alloy (tetrataenite), a promising candidate for rare-earth-free and low-cost permanent magnet applications, is attracting increasing attention from academic and industrial communities. Highly ordered single-phase L1₀-FeNi is difficult to synthesis efficiently because of its low chemical order-disorder transition temperature (200-320 °C). A non-equilibrium synthetic route utilizing a nitrogen topotactic reaction has been considered a valid approach, although the phase transformation mechanism is currently unknown. Herein, we investigated the basis of this reaction, namely the formation mechanism of the tetragonal FeNiN precursor phase during the nitridation of FeNi nanopowders. Detailed microstructure analysis revealed that the FeNiN precursor phase could preferentially nucleate at the nanotwinned region during nitridation and subsequently grow following a massive transformation, with high-index irrational orientation relationships and ledgewise growth motion detected at the migrating phase interface. This is the first report of a massive phase transformation detected in an Fe-Ni-N system and provides new insights into the phase transformation during the nitriding process. This work is expected to promote the synthetic optimization of fully ordered FeNi alloys for various magnetic applications.

Structure deposition and release

Deposited: 2016-11-27

Released: 2017-02-15

Revised: 2020-01-01

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 alpha T cell receptor alpha TRAV1	10 20 30 40 50 60 GQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRF 70 80 90 100 110 120 SSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVYQ 130 140 150 160 170 180 LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF 190 200 ACANAFNNSIIPEDTFFPSPESS

4. T cell receptor beta T cell receptor beta TRBV6	10 20 30 40 50 60 NAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEV 70 80 90 100 110 120 PNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLKN 130 140 150 160 170 180 VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE 190 200 210 220 230 240 QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA WGRAD

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]

5U16 assembly 1

Components

MHC Class I alpha chain [cif]

5U16 assembly 1

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

5U16 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/5u16

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

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.