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3RUG

Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 2.20Å 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

Cd1d with nkt alpha beta tcr

1. Beta 2 microglobulin
['B', 'D']
2. CD1d
['A', 'C']
3. T cell receptor alpha
TRAV13
['E']
4. T cell receptor beta
TRBV13
['F']

Species

Locus / Allele group

Non-classical MHC Class I molecule

Publication

A semi-invariant V��10+ T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties.

Uldrich AP, Patel O, Cameron G, Pellicci DG, Day EB, Sullivan LC, Kyparissoudis K, Kjer-Nielsen L, Vivian JP, Cao B, Brooks AG, Williams SJ, Illarionov P, Besra GS, Turner SJ, Porcelli SA, McCluskey J, Smyth MJ, Rossjohn J, Godfrey DI
Nat. Immunol. (2011) 12, 616-23 [doi:10.1038/ni.2051]  [pubmed:21666690] 

Electrochemically converting nitrate, a widespread water pollutant, back to valuable ammonia is a green and delocalized route for ammonia synthesis, and can be an appealing and supplementary alternative to the Haber-Bosch process. However, as there are other nitrate reduction pathways present, selectively guiding the reaction pathway towards ammonia is currently challenged by the lack of efficient catalysts. Here we report a selective and active nitrate reduction to ammonia on Fe single atom catalyst, with a maximal ammonia Faradaic efficiency of ~ 75% and a yield rate of up to ~ 20,000 μg h-1 mgcat.-1 (0.46 mmol h-1 cm-2). Our Fe single atom catalyst can effectively prevent the N-N coupling step required for N2 due to the lack of neighboring metal sites, promoting ammonia product selectivity. Density functional theory calculations reveal the reaction mechanisms and the potential limiting steps for nitrate reduction on atomically dispersed Fe sites.

Structure deposition and release

Deposited: 2011-05-05
Released: 2011-08-03
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
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
        70        80        90
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM
2. CD1d
CD1d
        10        20        30        40        50        60
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
        70        80        90       100       110       120
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
       130       140       150       160       170       180
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
       190       200       210       220       230       240
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
       250       260       270       280       290       300
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH

HH
3. T cell receptor alpha
T cell receptor alpha
TRAV13
        10        20        30        40        50        60
GQQVEQSPASLVLQEGENAELQCTYSTTLNSMQWFYQRPGGRLVSLLYSPSWAEQRGGRL
        70        80        90       100       110       120
TSSAASNESRSSLHISSSQITDSGTYLCAIASSSFSKLVFGQGTSLSVVPNIQNPDPAVY
       130       140       150       160       170       180
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
       190       200
FACANAFNNSIIPEDTFFPSPESS
4. T cell receptor beta
T cell receptor beta
TRBV13
        10        20        30        40        50        60
EAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDI
        70        80        90       100       110       120
PDGYKASRPSQENFSLILELASLSQTAVYFCASRLGGYEQYFGPGTRLTVLEDLKNVFPP
       130       140       150       160       170       180
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
       190       200       210       220       230       240
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA

D

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. 3RUG assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 3RUG assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3RUG assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3rug

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.