{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-mhc:SLA06100","locus":"sla-1","match_type":"histo:exact","name":"SLA-1*01:01","slug":"sla_1_01_01","species_stem":"SLA"},"beta":{}},"assemblies":{"1":{"assembly_name":"4elm_1","chains":["A","B","G","H","I"],"downloaded_at":"2022-11-09T14:43:37.644542"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","D"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM"},"cd1d":{"chains":["A","C"],"match_type":"histo:assign_chains","score":0.97,"sequence":"SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH"},"tcr_alpha":{"chains":["E"],"match_type":"stcrdab","sequence":"MQQKVQQSPESLSVPEGGMASLNCTSSDRNFQYFWWYRQHSGEGPKALMSIFSDGDKKEGRFTAHLNKASLHVSLHIRDSQPSDSALYFCAASEQNNYAQGLTFGLGTRVSVFPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS","subgroup":"TRAV7"},"tcr_beta":{"chains":["F"],"match_type":"stcrdab","sequence":"MGPKVLQIPSHQIIDMGQMVTLNCDPVSNHLYFYWYKQILGQQMEFLVNFYNGKVMEKSKLFKDQFSVERPDGSYFTLKIQPTALEDSAVYFCASSFWGAYAEQFFGPGTRLTVLEDLRNVTPPKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA","subgroup":"TRBV3"}},"chronology":{"deposition_date":"2012-04-11","deposition_year":2012,"release_date":"2012-07-25","release_year":2012,"revision_date":"2020-07-29","revision_year":2020},"class":"class_i","classical":false,"complex_type":"cd1d_with_nkt_alpha_beta_tcr","components":["cd1d","beta2m","tcr_alpha","tcr_beta"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"sla-1","manually_edited":{},"missing_residues":[],"page_title":"4ELM | Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor","pdb_code":"4elm","pdb_title":"Crystal structure of the mouse CD1d-lysosulfatide-hy19.3 TCR complex","peptide":{"actual_sequence":null,"epitope_info":{},"features":[],"full_sequence":null,"gap_info":{},"gapped_sequence":null,"length":{"numeric":null,"text":null},"unnatural_amino_acids":[]},"publication":{"abstract":"Selective metal coordination is central to the functions of metalloproteins:<sup>1,2</sup> each metalloprotein must pair with its cognate metallocofactor to fulfil its biological role<sup>3</sup>. However, achieving metal selectivity solely through a three-dimensional protein structure is a great challenge, because there is a limited set of metal-coordinating amino acid functionalities and proteins are inherently flexible, which impedes steric selection of metals<sup>3,4</sup>. Metal-binding affinities of natural proteins are primarily dictated by the electronic properties of metal ions and follow the Irving-Williams series<sup>5</sup> (Mn<sup>2+</sup>\u2009<\u2009Fe<sup>2+</sup>\u2009<\u2009Co<sup>2+</sup>\u2009<\u2009Ni<sup>2+</sup>\u2009<\u2009Cu<sup>2+</sup>\u2009>\u2009Zn<sup>2+</sup>) with few exceptions<sup>6,7</sup>. Accordingly, metalloproteins overwhelmingly bind Cu<sup>2+</sup> and Zn<sup>2+</sup> in isolation, regardless of the nature of their active sites and their cognate metal ions<sup>1,3,8</sup>. This led organisms to evolve complex homeostatic machinery and non-equilibrium strategies to achieve correct metal speciation<sup>1,3,8-10</sup>. Here we report an artificial dimeric protein, (AB)<sub>2</sub>, that thermodynamically overcomes the Irving-Williams restrictions in vitro and in cells, favouring the binding of lower-Irving-Williams transition metals over Cu<sup>2+</sup>, the most dominant ion in the Irving-Williams series. Counter to the convention in molecular design of achieving specificity through structural preorganization, (AB)<sub>2</sub> was deliberately designed to be flexible. This flexibility enabled (AB)<sub>2</sub> to adopt mutually exclusive, metal-dependent conformational states, which led to the discovery of structurally coupled coordination sites that disfavour Cu<sup>2+</sup> ions by enforcing an unfavourable coordination geometry. Aside from highlighting flexibility as a valuable element in protein design, our results illustrate design principles for constructing selective metal sequestration agents.","bibjson":{"author":[{"initials":"E","lastname":"Girardi","name":"Girardi E"},{"initials":"I","lastname":"Maricic","name":"Maricic I"},{"initials":"J","lastname":"Wang","name":"Wang J"},{"initials":"TT","lastname":"Mac","name":"Mac TT"},{"initials":"P","lastname":"Iyer","name":"Iyer P"},{"initials":"V","lastname":"Kumar","name":"Kumar V"},{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"}],"identifier":[{"id":"10.1038/ni.2371","type":"doi"},{"id":"22820602","type":"pubmed"}],"issue":["9"],"journal":{"iso_abbreviation":"Nat. Immunol.","name":""},"pages":["851-6"],"title":"Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.","type":"article","url":"http://www.nature.com/articles/ni.2371","volume":["13"],"year":[2012]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"3.48","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4elm"},"rcsb":{"url":"https://www.rcsb.org/structure/4elm"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=4elm"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":{"alpha":{"chains":["E"],"subgroup":"TRAV7"},"beta":{"chains":["F"],"subgroup":"TRBV3"},"pdb_code":"4elm"},"title":"Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 3.48&#8491; resolution","unique_chain_count":4}}