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3SDC

Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 3.10Å 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']
2. CD1d
['A']
3. T cell receptor alpha
TRAV11
['C']
4. T cell receptor beta
TRBV19
['D']

Species

Locus / Allele group

Non-classical MHC Class I molecule

Publication

Recognition of ��-linked self glycolipids mediated by natural killer T cell antigen receptors.

Pellicci DG, Clarke AJ, Patel O, Mallevaey T, Beddoe T, Le Nours J, Uldrich AP, McCluskey J, Besra GS, Porcelli SA, Gapin L, Godfrey DI, Rossjohn J
Nat. Immunol. (2011) 12, 827-33 [doi:10.1038/ni.2076]  [pubmed:21804559] 

Electrocatalytic urea synthesis emerged as the promising alternative of Haber-Bosch process and industrial urea synthetic protocol. Here, we report that a diatomic catalyst with bonded Fe-Ni pairs can significantly improve the efficiency of electrochemical urea synthesis. Compared with isolated diatomic and single-atom catalysts, the bonded Fe-Ni pairs act as the efficient sites for coordinated adsorption and activation of multiple reactants, enhancing the crucial C-N coupling thermodynamically and kinetically. The performance for urea synthesis up to an order of magnitude higher than those of single-atom and isolated diatomic electrocatalysts, a high urea yield rate of 20.2 mmol h-1 g-1 with corresponding Faradaic efficiency of 17.8% has been successfully achieved. A total Faradaic efficiency of about 100% for the formation of value-added urea, CO, and NH3 was realized. This work presents an insight into synergistic catalysis towards sustainable urea synthesis via identifying and tailoring the atomic site configurations.

Structure deposition and release

Deposited: 2011-06-09
Released: 2011-10-05
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
TRAV11
        10        20        30        40        50        60
TQVEQSPQSLVVRQGENSVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGR
        70        80        90       100       110       120
YSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDP
       130       140       150       160       170       180
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
       190       200
KSDFACANAFNNSIIPEDTFFPSPESS
4. T cell receptor beta
T cell receptor beta
TRBV19
        10        20        30        40        50        60
HMGGIITQTPKFLIGQEGQKLTLKCQQNFNHDTMYWYRQDSGKGLRLIYYSYGAGSTEKG
        70        80        90       100       110       120
DLSEGYDASREKKSSFSLTVTSAQKNEMAVFLCASGSLLDVREVFFGKGTRLTVVEDLKN
       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]
  1. 3SDC assembly 1  

Components

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

Derived data

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

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.