{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:47:21Z","timestamp":1782280041316,"version":"3.54.5"},"posted":{"date-parts":[[2025,5,13]]},"group-title":"Biochemistry","reference-count":67,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T00:00:00Z","timestamp":1747094400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01GM102262"],"award-info":[{"award-number":["R01GM102262"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R35GM150644"],"award-info":[{"award-number":["R35GM150644"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,28]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Numerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have been reported, with variable crystal lattice contacts and chemical crystallization conditions. Here, we report a unique crystal structure of Src SH3 domain in trigonal space group\n                  <jats:italic>H<\/jats:italic>\n                  3\n                  <jats:sub>2<\/jats:sub>\n                  to 1.45 \u00c5 resolution. Crystal packing and anomalous scattering reveal that this crystal form is mediated by two ordered nickel ions provided by the crystallization buffer. Nickel coordination occurs in a 2:2 stoichiometry which dimerizes two SH3 domain monomers across a pseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, a surface-exposed histidine residue, and ordered water molecules. This study provides an example of metal binding by N-terminal protein residues that contrasts the amino terminal copper and nickel binding (ATCUN) motif and is an alternative avenue for crystallization of the Src SH3 domain.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>STRUCTURED ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Numerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have been reported, with variable crystal lattice contacts and chemical crystallization conditions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and Methods<\/jats:title>\n                    <jats:p>\n                      We crystallize the c-Src SH3 domain in a crystallization buffer containing NiCl\n                      <jats:sub>2<\/jats:sub>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A unique crystal structure of Src SH3 domain in trigonal space group\n                      <jats:italic>H<\/jats:italic>\n                      3\n                      <jats:sub>2<\/jats:sub>\n                      to 1.45 \u00c5 resolution is determined. Crystal packing and anomalous scattering reveal that this crystal form is mediated by two ordered nickel ions provided by the crystallization buffer. Nickel coordination occurs in a 2:2 stoichiometry which dimerizes two SH3 domain monomers across a pseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, a surface-exposed histidine residue, and ordered water molecules.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>This study provides an example of metal-mediated crystallization and metal binding by N-terminal protein residues that contrasts the amino terminal copper and nickel binding (ATCUN) motif.<\/jats:p>\n                  <\/jats:sec>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Alternative avenues for helps widen the potential for future crystallography-based studies of the c-Src SH3 domain.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.05.08.652639","type":"posted-content","created":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T08:25:11Z","timestamp":1747124711000},"source":"Crossref","is-referenced-by-count":0,"title":["Nickel binding to c-Src SH3 domain facilitates crystallization"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5440-5955","authenticated-orcid":false,"given":"Xander","family":"Calicdan","sequence":"first","affiliation":[{"name":"Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3215-0831","authenticated-orcid":false,"given":"Oriana S.","family":"Fisher","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6594-0835","authenticated-orcid":false,"given":"Byung Hak","family":"Ha","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2862-1637","authenticated-orcid":false,"given":"Titus J.","family":"Boggon","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Yale University, New Haven, CT, USA"},{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0453-6104","authenticated-orcid":false,"given":"Amy L.","family":"Stiegler","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041123503966000_2025.05.08.652639v2.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2004.03.011"},{"key":"2026041123503966000_2025.05.08.652639v2.2","doi-asserted-by":"publisher","DOI":"10.2741\/3053"},{"key":"2026041123503966000_2025.05.08.652639v2.3","doi-asserted-by":"publisher","DOI":"10.1038\/332272a0"},{"key":"2026041123503966000_2025.05.08.652639v2.4","doi-asserted-by":"crossref","unstructured":"Mehrabipour, M. ; Jasemi, N. S. K. ; Dvorsky, R. ; Ahmadian, M. R ., A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023, 12 (16).","DOI":"10.3390\/cells12162054"},{"key":"2026041123503966000_2025.05.08.652639v2.5","doi-asserted-by":"crossref","unstructured":"Kazemein Jasemi , N. S.; Mehrabipour , M.; Magdalena Estirado , E.; Brunsveld , L.; Dvorsky , R.; Ahmadian , M. R., Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily. Cells 2024, 13 (2).","DOI":"10.3390\/cells13020195"},{"key":"2026041123503966000_2025.05.08.652639v2.6","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1993.tb05922.x"},{"key":"2026041123503966000_2025.05.08.652639v2.7","doi-asserted-by":"publisher","DOI":"10.1126\/science.1280858"},{"key":"2026041123503966000_2025.05.08.652639v2.8","doi-asserted-by":"publisher","DOI":"10.1038\/359851a0"},{"key":"2026041123503966000_2025.05.08.652639v2.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2017.07.017"},{"key":"2026041123503966000_2025.05.08.652639v2.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2012.04.042"},{"key":"2026041123503966000_2025.05.08.652639v2.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32541-4"},{"key":"2026041123503966000_2025.05.08.652639v2.12","doi-asserted-by":"publisher","DOI":"10.1126\/science.7526465"},{"key":"2026041123503966000_2025.05.08.652639v2.13","doi-asserted-by":"publisher","DOI":"10.1038\/372375a0"},{"key":"2026041123503966000_2025.05.08.652639v2.14","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0894-546"},{"key":"2026041123503966000_2025.05.08.652639v2.15","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(94)90367-0"},{"key":"2026041123503966000_2025.05.08.652639v2.16","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1208081"},{"key":"2026041123503966000_2025.05.08.652639v2.17","doi-asserted-by":"publisher","DOI":"10.1038\/385595a0"},{"key":"2026041123503966000_2025.05.08.652639v2.18","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1996.tb00871.x"},{"key":"2026041123503966000_2025.05.08.652639v2.19","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.271.35.21365"},{"key":"2026041123503966000_2025.05.08.652639v2.20","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1995.tb07024.x"},{"key":"2026041123503966000_2025.05.08.652639v2.21","doi-asserted-by":"publisher","DOI":"10.1126\/science.1379745"},{"key":"2026041123503966000_2025.05.08.652639v2.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-53447-0"},{"key":"2026041123503966000_2025.05.08.652639v2.23","doi-asserted-by":"publisher","DOI":"10.1126\/science.283.5402.655"},{"key":"2026041123503966000_2025.05.08.652639v2.24","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(95)00073-X"},{"key":"2026041123503966000_2025.05.08.652639v2.25","doi-asserted-by":"publisher","DOI":"10.1107\/S1600577520016173"},{"key":"2026041123503966000_2025.05.08.652639v2.26","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444911007773"},{"key":"2026041123503966000_2025.05.08.652639v2.27","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909047337"},{"key":"2026041123503966000_2025.05.08.652639v2.28","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444913000061"},{"key":"2026041123503966000_2025.05.08.652639v2.29","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444912001308"},{"key":"2026041123503966000_2025.05.08.652639v2.30","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889807021206"},{"key":"2026041123503966000_2025.05.08.652639v2.31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0113224"},{"key":"2026041123503966000_2025.05.08.652639v2.32","doi-asserted-by":"publisher","DOI":"10.1107\/S090744490705024X"},{"key":"2026041123503966000_2025.05.08.652639v2.33","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444904019158"},{"key":"2026041123503966000_2025.05.08.652639v2.34","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360221211"},{"key":"2026041123503966000_2025.05.08.652639v2.35","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4525"},{"key":"2026041123503966000_2025.05.08.652639v2.36","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444913001479"},{"key":"2026041123503966000_2025.05.08.652639v2.37","doi-asserted-by":"crossref","unstructured":"El Omari , K.; Forsyth , I.; Duman , R.; Orr , C. M.; Mykhaylyk , V.; Mancini , E. J.; Wagner , A., Utilizing anomalous signals for element identification in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024.","DOI":"10.1107\/S2059798324008659"},{"key":"2026041123503966000_2025.05.08.652639v2.38","unstructured":"Sasaki, S. a. N. L. f. H. E. P., Tsukuba, Ibaraki (Japan), Numerical Tables of Anomalous Scattering Factors Calculated by the Cromer and Liberman\u2019s Method. 1989."},{"key":"2026041123503966000_2025.05.08.652639v2.39","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444911007281"},{"key":"2026041123503966000_2025.05.08.652639v2.40","doi-asserted-by":"publisher","DOI":"10.1002\/PRO.3943"},{"key":"2026041123503966000_2025.05.08.652639v2.41","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.01456"},{"key":"2026041123503966000_2025.05.08.652639v2.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.05.022"},{"key":"2026041123503966000_2025.05.08.652639v2.43","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444904026460"},{"key":"2026041123503966000_2025.05.08.652639v2.44","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq366"},{"key":"2026041123503966000_2025.05.08.652639v2.45","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts246"},{"key":"2026041123503966000_2025.05.08.652639v2.46","doi-asserted-by":"crossref","unstructured":"Opdam, L. V. ; Polanco, E. A. ; de Regt, B. ; Lambertina, N. ; Bakker, C. ; Bonnet, S. ; Pandit, A ., A screening method for binding synthetic metallo-complexes to haem proteins. Anal Biochem 2022, 653, 114788.","DOI":"10.1016\/j.ab.2022.114788"},{"key":"2026041123503966000_2025.05.08.652639v2.47","doi-asserted-by":"publisher","DOI":"10.1039\/C4MT00033A"},{"key":"2026041123503966000_2025.05.08.652639v2.48","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20265"},{"key":"2026041123503966000_2025.05.08.652639v2.49","doi-asserted-by":"publisher","DOI":"10.1021\/bi00307a046"},{"issue":"12","key":"2026041123503966000_2025.05.08.652639v2.50","first-page":"101792","article-title":"Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry","volume":"23","year":"2020","journal-title":"Biology, and Medicine. iScience"},{"issue":"1","key":"2026041123503966000_2025.05.08.652639v2.51","first-page":"14","article-title":"Kinetics of Cu(II) complexation by ATCUN\/NTS and related peptides: a gold mine of novel ideas for copper biology","volume":"51","year":"2021","journal-title":"Dalton Trans"},{"key":"2026041123503966000_2025.05.08.652639v2.52","doi-asserted-by":"publisher","DOI":"10.1007\/s00775-020-01785-0"},{"key":"2026041123503966000_2025.05.08.652639v2.53","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444913001522"},{"key":"2026041123503966000_2025.05.08.652639v2.54","first-page":"33","article-title":"Fragment screening using X-ray crystallography","volume":"317","year":"2012","journal-title":"Top Curr Chem"},{"key":"2026041123503966000_2025.05.08.652639v2.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbiomolbio.2014.08.004"},{"key":"2026041123503966000_2025.05.08.652639v2.56","doi-asserted-by":"publisher","DOI":"10.1110\/ps.072914007"},{"key":"2026041123503966000_2025.05.08.652639v2.57","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2006.09.005"},{"key":"2026041123503966000_2025.05.08.652639v2.58","doi-asserted-by":"publisher","DOI":"10.1002\/pro.550"},{"key":"2026041123503966000_2025.05.08.652639v2.59","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0607674103"},{"key":"2026041123503966000_2025.05.08.652639v2.60","doi-asserted-by":"publisher","DOI":"10.1110\/ps.072851407"},{"key":"2026041123503966000_2025.05.08.652639v2.61","doi-asserted-by":"publisher","DOI":"10.1021\/ar900273t"},{"key":"2026041123503966000_2025.05.08.652639v2.62","doi-asserted-by":"publisher","DOI":"10.1002\/pro.727"},{"key":"2026041123503966000_2025.05.08.652639v2.63","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3214"},{"key":"2026041123503966000_2025.05.08.652639v2.64","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560040925"},{"key":"2026041123503966000_2025.05.08.652639v2.65","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2018.018"},{"key":"2026041123503966000_2025.05.08.652639v2.66","doi-asserted-by":"crossref","unstructured":"Pakharukova, N. ; Thomas, B. N. ; Bansia, H. ; Li, L. ; Abzalimov, R. R. ; Kim, J. ; Kahsai, A. W. ; Pani, B. ; Bassford, D. K. ; Liu, S. ; Zhang, X. ; des Georges, A. ; Lefkowitz, R. J ., Beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy. bioRxiv 2024.","DOI":"10.1101\/2024.07.31.605623"},{"key":"2026041123503966000_2025.05.08.652639v2.67","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909042073"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.05.08.652639","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T04:55:41Z","timestamp":1782276941000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.08.652639"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,13]]},"references-count":67,"URL":"https:\/\/doi.org\/10.1101\/2025.05.08.652639","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.2174\/0109298665417324250929120040","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,5,13]]},"subtype":"preprint"}}