{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:24:23Z","timestamp":1772173463091,"version":"3.50.1"},"reference-count":150,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2025,4,14]],"date-time":"2025-04-14T00:00:00Z","timestamp":1744588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"NIH"},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["grant 2346274"],"award-info":[{"award-number":["grant 2346274"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of these\n                    <jats:italic>systems<\/jats:italic>\n                    . The \u201cIgStrand numbering scheme\u201d enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the\n                    <jats:italic>\u201cIg-fold irreducible structural signature\u201d<\/jats:italic>\n                    shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly, it sheds light on the robust\n                    <jats:italic>Ig protein folding algorithm<\/jats:italic>\n                    used by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies or origin. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an \u201cIg-extended\u201d architecture are given. Applications in protein engineering around the Ig-architecture are straightforward based on the universal numbering.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012813","type":"journal-article","created":{"date-parts":[[2025,4,14]],"date-time":"2025-04-14T13:25:01Z","timestamp":1744637101000},"page":"e1012813","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes"],"prefix":"10.1371","volume":"21","author":[{"given":"Caesar","family":"Tawfeeq","sequence":"first","affiliation":[]},{"given":"Jiyao","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Umesh","family":"Khaniya","sequence":"additional","affiliation":[]},{"given":"Thomas","family":"Madej","sequence":"additional","affiliation":[]},{"given":"James","family":"Song","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7333-6793","authenticated-orcid":true,"given":"Ravinder","family":"Abrol","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2942-2712","authenticated-orcid":true,"given":"Philippe","family":"Youkharibache","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2025,4,14]]},"reference":[{"issue":"6822","key":"pcbi.1012813.ref001","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"International Human Genome Sequencing Consortium","year":"2001","journal-title":"Nature"},{"issue":"4","key":"pcbi.1012813.ref002","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1007\/PL00006318","article-title":"The immunoglobulin superfamily: an insight on its tissular, species, and functional diversity","volume":"46","author":"DM Halaby","year":"1998","journal-title":"J Mol Evol"},{"issue":"5","key":"pcbi.1012813.ref003","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1002\/eji.201746984","article-title":"Immunoglobulin superfamily members encoded by viruses and their multiple roles in immune evasion","volume":"47","author":"D Farr\u00e9","year":"2017","journal-title":"Eur J Immunol"},{"issue":"2","key":"pcbi.1012813.ref004","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.jmb.2006.03.043","article-title":"Ig-like domains on bacteriophages: a tale of promiscuity and deceit","volume":"359","author":"JS Fraser","year":"2006","journal-title":"J Mol Biol"},{"issue":"9","key":"pcbi.1012813.ref005","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1002\/pro.5560050923","article-title":"Members of the immunoglobulin superfamily in bacteria","volume":"5","author":"A Bateman","year":"1996","journal-title":"Protein Sci"},{"key":"pcbi.1012813.ref006","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1111\/j.0105-2896.2004.00122.x","article-title":"Immunoglobulin superfamily receptors in protochordates: before RAG time","volume":"198","author":"L Du Pasquier","year":"2004","journal-title":"Immunol Rev"},{"issue":"5742","key":"pcbi.1012813.ref007","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.1126\/science.1116887","article-title":"Extensive diversity of Ig-superfamily proteins in the immune system of insects","volume":"309","author":"FL Watson","year":"2005","journal-title":"Science"},{"key":"pcbi.1012813.ref008","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.imlet.2003.10.012","article-title":"Speculations on the origin of the vertebrate immune system","volume":"92","author":"L Du Pasquier","year":"2004","journal-title":"Immunol Lett"},{"key":"pcbi.1012813.ref009","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/978-3-642-59674-2_8","article-title":"The Phylogenetic Origin of Antigen-Specific Receptors.","volume-title":"Origin and Evolution of the Vertebrate Immune System [Internet]","author":"L. Du Pasquier","year":"2000"},{"issue":"4","key":"pcbi.1012813.ref010","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1016\/j.cell.2006.02.001","article-title":"The evolution of adaptive immune systems","volume":"124","author":"MD Cooper","year":"2006","journal-title":"Cell"},{"key":"pcbi.1012813.ref011","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/B978-0-12-809843-1.00002-4","article-title":"Chapter 2 - Principles of Immunophenotyping.","volume-title":"Atlas of Hematopathology (Second Edition) [Internet]","author":"F Naeim","year":"2018"},{"issue":"6","key":"pcbi.1012813.ref012","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1007\/s00251-023-01319-3","article-title":"Genomic view of the origins of cell-mediated immunity","volume":"75","author":"ME Janes","year":"2023","journal-title":"Immunogenetics"},{"key":"pcbi.1012813.ref013","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1146\/annurev.neuro.29.051605.113034","article-title":"Adhesion molecules in the nervous system: structural insights into function and diversity","volume":"30","author":"L Shapiro","year":"2007","journal-title":"Annu Rev Neurosci"},{"issue":"3","key":"pcbi.1012813.ref014","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1016\/j.cell.2020.04.010","article-title":"Adhesion protein structure, molecular affinities, and principles of cell-cell recognition","volume":"181","author":"B Honig","year":"2020","journal-title":"Cell"},{"key":"pcbi.1012813.ref015","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/978-981-13-9077-7_4","article-title":"Cell Adhesion Molecules.","volume-title":"Advances in membrane proteins: building, signaling and malfunction [Internet]","author":"X Tong","year":"2019"},{"key":"pcbi.1012813.ref016","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.conb.2017.05.010","article-title":"Neural immunoglobulin superfamily interaction networks","volume":"45","author":"K Zinn","year":"2017","journal-title":"Curr Opin Neurobiol"},{"issue":"1","key":"pcbi.1012813.ref017","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1002\/dvdy.512","article-title":"Structure and evolution of neuronal wiring receptors and ligands","volume":"252","author":"E Cort\u00e9s","year":"2023","journal-title":"Dev Dyn"},{"issue":"20","key":"pcbi.1012813.ref018","doi-asserted-by":"crossref","first-page":"9837","DOI":"10.1073\/pnas.1818631116","article-title":"Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence","volume":"116","author":"S Cheng","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"pcbi.1012813.ref019","article-title":"Interactions between the Ig-Superfamily Proteins DIP-\u03b1 and Dpr6\/10 regulate assembly of neural circuits","volume":"100","author":"S Xu","year":"2018","journal-title":"Neuron"},{"issue":"34","key":"pcbi.1012813.ref020","doi-asserted-by":"crossref","first-page":"e2206175119","DOI":"10.1073\/pnas.2206175119","article-title":"On the formation of ordered protein assemblies in cell-cell interfaces","volume":"119","author":"N Boni","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"pcbi.1012813.ref021","doi-asserted-by":"crossref","first-page":"278","DOI":"10.5483\/BMBRep.2008.41.4.278","article-title":"Vascular endothelial growth factor-dependent and -independent regulation of angiogenesis","volume":"41","author":"M Shibuya","year":"2008","journal-title":"BMB Rep"},{"issue":"10","key":"pcbi.1012813.ref022","doi-asserted-by":"crossref","first-page":"a009092","DOI":"10.1101\/cshperspect.a009092","article-title":"VEGFR and type-V RTK activation and signaling","volume":"5","author":"M Shibuya","year":"2013","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"4","key":"pcbi.1012813.ref023","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1161\/CIRCRESAHA.108.188144","article-title":"Guidance of vascular development: lessons from the nervous system","volume":"104","author":"B Larriv\u00e9e","year":"2009","journal-title":"Circ Res"},{"issue":"5234","key":"pcbi.1012813.ref024","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1126\/science.270.5234.293","article-title":"Titins: giant proteins in charge of muscle ultrastructure and elasticity","volume":"270","author":"S Labeit","year":"1995","journal-title":"Science"},{"issue":"6901","key":"pcbi.1012813.ref025","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1038\/nature00938","article-title":"Reverse engineering of the giant muscle protein titin","volume":"418","author":"H Li","year":"2002","journal-title":"Nature"},{"key":"pcbi.1012813.ref026","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1146\/annurev-physiol-021317-121254","article-title":"The work of titin protein folding as a major driver in muscle contraction","volume":"80","author":"EC Eckels","year":"2018","journal-title":"Annu Rev Physiol"},{"issue":"4","key":"pcbi.1012813.ref027","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.jmb.2014.12.017","article-title":"Titin and obscurin: giants holding hands and discovery of a new Ig domain subset","volume":"427","author":"GM Benian","year":"2015","journal-title":"J Mol Biol"},{"issue":"1","key":"pcbi.1012813.ref028","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/s41467-017-02528-7","article-title":"Disulfide isomerization reactions in titin immunoglobulin domains enable a mode of protein elasticity","volume":"9","author":"D Giganti","year":"2018","journal-title":"Nat Commun"},{"key":"pcbi.1012813.ref029","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1146\/annurev-biochem-052521-042909","article-title":"Structural biochemistry of muscle contraction","volume":"92","author":"Z Wang","year":"2023","journal-title":"Annu Rev Biochem"},{"issue":"9","key":"pcbi.1012813.ref030","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1091\/mbc.e14-02-0733","article-title":"Systematic identification of pathological lamin A interactors","volume":"25","author":"TA Dittmer","year":"2014","journal-title":"Mol Biol Cell"},{"issue":"8","key":"pcbi.1012813.ref031","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1002\/cm.20385","article-title":"Cytoplasmic Ig-domain proteins: cytoskeletal regulators with a role in human disease","volume":"66","author":"CA Otey","year":"2009","journal-title":"Cell Motil Cytoskeleton"},{"issue":"51","key":"pcbi.1012813.ref032","doi-asserted-by":"crossref","first-page":"19659","DOI":"10.1074\/jbc.RA118.004142","article-title":"Identification of two principal amyloid-driving segments in variable domains of Ig light chains in systemic light-chain amyloidosis","volume":"293","author":"B Brumshtein","year":"2018","journal-title":"J Biol Chem"},{"issue":"1","key":"pcbi.1012813.ref033","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1038\/s41467-023-36791-8","article-title":"Disease-relevant \u03b22-microglobulin variants share a common amyloid fold","volume":"14","author":"M Wilkinson","year":"2023","journal-title":"Nat Commun"},{"issue":"5","key":"pcbi.1012813.ref034","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1016\/j.autrev.2017.12.005","article-title":"Skeletal muscle cells actively shape (auto)immune responses","volume":"17","author":"AM Afzali","year":"2018","journal-title":"Autoimmun Rev"},{"key":"pcbi.1012813.ref035","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.ebiom.2019.10.034","article-title":"Skeletal muscle as potential central link between sarcopenia and immune senescence","volume":"49","author":"C Nelke","year":"2019","journal-title":"EBioMedicine"},{"issue":"6","key":"pcbi.1012813.ref036","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/ni1078","article-title":"Elaborate interactions between the immune and nervous systems","volume":"5","author":"L Steinman","year":"2004","journal-title":"Nat Immunol"},{"key":"pcbi.1012813.ref037","doi-asserted-by":"crossref","first-page":"916","DOI":"10.3389\/fnins.2019.00916","article-title":"Role of the immune system in the development of the central nervous system","volume":"13","author":"K Morimoto","year":"2019","journal-title":"Front Neurosci"},{"issue":"1","key":"pcbi.1012813.ref038","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1152\/physrev.00039.2016","article-title":"Neuroimmune interactions: from the brain to the immune system and vice versa","volume":"98","author":"R Dantzer","year":"2018","journal-title":"Physiol Rev"},{"issue":"11","key":"pcbi.1012813.ref039","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1038\/nm.2234","article-title":"Interactions between the immune and nervous systems in pain","volume":"16","author":"K Ren","year":"2010","journal-title":"Nat Med"},{"issue":"4","key":"pcbi.1012813.ref040","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/S0031-6997(24)01470-4","article-title":"The sympathetic nerve\u2014an integrative interface between two supersystems: the brain and the immune system","volume":"52","author":"IJ Elenkov","year":"2000","journal-title":"Pharmacol Rev"},{"issue":"8","key":"pcbi.1012813.ref041","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1038\/s41577-021-00508-z","article-title":"Neuromodulation by the immune system: a focus on cytokines","volume":"21","author":"AF Salvador","year":"2021","journal-title":"Nat Rev Immunol"},{"issue":"7965","key":"pcbi.1012813.ref042","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/s41586-023-05968-y","article-title":"The neuroscience of cancer","volume":"618","author":"R Mancusi","year":"2023","journal-title":"Nature"},{"issue":"7908","key":"pcbi.1012813.ref043","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41586-022-04673-6","article-title":"Neuroimmune cardiovascular interfaces control atherosclerosis","volume":"605","author":"SK Mohanta","year":"2022","journal-title":"Nature"},{"issue":"10","key":"pcbi.1012813.ref044","first-page":"e22509","article-title":"The role of semaphorins in cardiovascular diseases: potential therapeutic targets and novel biomarkers","volume":"36","author":"Z Yin","year":"2022","journal-title":"FASEB J"},{"issue":"1","key":"pcbi.1012813.ref045","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s41232-023-00281-7","article-title":"Pathophysiological functions of semaphorins in the sympathetic nervous system","volume":"43","author":"Y Mizuno","year":"2023","journal-title":"Inflamm Regen"},{"issue":"2","key":"pcbi.1012813.ref046","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/0022-2836(82)90179-6","article-title":"Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains","volume":"160","author":"AM Lesk","year":"1982","journal-title":"J Mol Biol"},{"issue":"4","key":"pcbi.1012813.ref047","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1006\/jmbi.1994.1312","article-title":"Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains","volume":"238","author":"Y Harpaz","year":"1994","journal-title":"J Mol Biol"},{"issue":"1","key":"pcbi.1012813.ref048","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1146\/annurev.iy.06.040188.002121","article-title":"The immunoglobulin superfamily\u2014domains for cell surface recognition","volume":"6","author":"AF Williams","year":"1988","journal-title":"Annu Rev Immunol"},{"issue":"12","key":"pcbi.1012813.ref049","doi-asserted-by":"crossref","first-page":"3305","DOI":"10.1073\/pnas.70.12.3305","article-title":"Three-dimensional structure of the Fab\u2019 fragment of a human immunoglobulin at 2,8-A resolution","volume":"70","author":"RJ Poljak","year":"1973","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1012813.ref050","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1016\/S0021-9258(17)38249-2","article-title":"Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin new at 2.0 A resolution","volume":"253","author":"FA Saul","year":"1978","journal-title":"J Biol Chem"},{"issue":"9","key":"pcbi.1012813.ref051","doi-asserted-by":"crossref","first-page":"3440","DOI":"10.1073\/pnas.71.9.3440","article-title":"The three-dimensional structure of the fab\u2019 fragment of a human myeloma immunoglobulin at 2.0-angstrom resolution","volume":"71","author":"RJ Poljak","year":"1974","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5516","key":"pcbi.1012813.ref052","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1038\/256373a0","article-title":"Three-dimensional structure, function and genetic control of immunoglobulins","volume":"256","author":"RJ Poljak","year":"1975","journal-title":"Nature"},{"key":"pcbi.1012813.ref053","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1146\/annurev.iy.06.040188.003011","article-title":"Three-dimensional structure of antibodies","volume":"6","author":"PM Alzari","year":"1988","journal-title":"Annu Rev Immunol"},{"key":"pcbi.1012813.ref054","first-page":"775","article-title":"Domains, Immunoglobulin-Type.","volume-title":"Encyclopedia of Immunology (Second Edition) [Internet]","author":"PM. Alzari","year":"1998"},{"issue":"2","key":"pcbi.1012813.ref055","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.imlet.2010.09.016","article-title":"Towards a comprehensive human cell-surface immunome database","volume":"134","author":"MC D\u00edaz-Ramos","year":"2011","journal-title":"Immunol Lett"},{"issue":"46","key":"pcbi.1012813.ref056","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.1808790115","article-title":"The in silico human surfaceome","volume":"115","author":"D Bausch-Fluck","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1012813.ref057","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2020.06.007","article-title":"The Immunoglobulin superfamily receptome defines cancer-relevant networks associated with clinical outcome","volume":"182","author":"E Verschueren","year":"2020","journal-title":"Cell"},{"issue":"7922","key":"pcbi.1012813.ref058","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/s41586-022-05028-x","article-title":"A physical wiring diagram for the human immune system","volume":"608","author":"J Shilts","year":"2022","journal-title":"Nature"},{"issue":"1","key":"pcbi.1012813.ref059","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1093\/nar\/gkg087","article-title":"CDD: a curated Entrez database of conserved domain alignments","volume":"31","author":"A Marchler-Bauer","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1012813.ref060","article-title":"CDD\/SPARCLE: the conserved domain database in 2020","volume":"48","author":"S Lu","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1012813.ref061","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/978-1-4939-9161-7_10","article-title":"Protodomains: symmetry-related supersecondary structures in proteins and self-complementarity","volume":"1958","author":"P Youkharibache","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"6","key":"pcbi.1012813.ref062","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/S0161-5890(99)00032-2","article-title":"Conservation of cys-cys trp structural triads and their geometry in the protein domains of immunoglobulin superfamily members","volume":"36","author":"TR Ioerger","year":"1999","journal-title":"Mol Immunol"},{"issue":"15","key":"pcbi.1012813.ref063","doi-asserted-by":"crossref","first-page":"6793","DOI":"10.1073\/pnas.92.15.6793","article-title":"Considerations on the folding topology and evolutionary origin of cadherin domains","volume":"92","author":"L Shapiro","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1012813.ref064","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1111\/j.1432-1033.1974.tb03576.x","article-title":"Crystal and molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI","volume":"45","author":"O Epp","year":"1974","journal-title":"Eur J Biochem"},{"issue":"22","key":"pcbi.1012813.ref065","doi-asserted-by":"crossref","first-page":"4943","DOI":"10.1021\/bi00693a025","article-title":"The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-A resolution","volume":"14","author":"O Epp","year":"1975","journal-title":"Biochemistry"},{"issue":"6","key":"pcbi.1012813.ref066","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/nsmb.2051","article-title":"Molecular design principles underlying \u03b2-strand swapping in the adhesive dimerization of cadherins","volume":"18","author":"J Vendome","year":"2011","journal-title":"Nat Struct Mol Biol"},{"issue":"6","key":"pcbi.1012813.ref067","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.tcb.2012.03.004","article-title":"Thinking outside the cell: how cadherins drive adhesion","volume":"22","author":"J Brasch","year":"2012","journal-title":"Trends in Cell Biology"},{"issue":"4","key":"pcbi.1012813.ref068","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures","volume":"247","author":"AG Murzin","year":"1995","journal-title":"J Mol Biol"},{"key":"pcbi.1012813.ref069","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkab1054","article-title":"SCOPe: improvements to the structural classification of proteins\u2014extended database to facilitate variant interpretation and machine learning","volume":"50","author":"JM Chandonia","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"pcbi.1012813.ref070","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","article-title":"CATH--a hierarchic classification of protein domain structures","volume":"5","author":"CA Orengo","year":"1997","journal-title":"Structure"},{"key":"pcbi.1012813.ref071","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa1079","article-title":"CATH: increased structural coverage of functional space","volume":"49","author":"I Sillitoe","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"pcbi.1012813.ref072","doi-asserted-by":"crossref","first-page":"e1003926","DOI":"10.1371\/journal.pcbi.1003926","article-title":"ECOD: an evolutionary classification of protein domains. Vol. 10","volume":"10","author":"H Cheng","year":"3926","journal-title":"PLoS Comput. Biol"},{"issue":"7","key":"pcbi.1012813.ref073","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1002\/prot.24818","article-title":"Manual classification strategies in the ECOD database","volume":"83","author":"H Cheng","year":"2015","journal-title":"Proteins"},{"issue":"4","key":"pcbi.1012813.ref074","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/S0022-2836(84)71582-8","article-title":"The immunoglobulin fold. 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Biol"},{"issue":"2","key":"pcbi.1012813.ref094","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1093\/bioinformatics\/btv552","article-title":"ANARCI: antigen receptor numbering and receptor classification","volume":"32","author":"J Dunbar","year":"2016","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1012813.ref095","doi-asserted-by":"crossref","first-page":"133","DOI":"10.2174\/138920209787847014","article-title":"The arrestin fold: variations on a theme","volume":"10","author":"L Aubry","year":"2009","journal-title":"Curr Genomics"},{"issue":"4","key":"pcbi.1012813.ref096","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1111\/jnc.15232","article-title":"The finger loop as an activation sensor in arrestin","volume":"157","author":"SA Vishnivetskiy","year":"2021","journal-title":"J Neurochem"},{"issue":"5","key":"pcbi.1012813.ref097","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1186\/gb-2011-12-5-222","article-title":"The lamin protein 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Fass","year":"1997","journal-title":"Science"},{"issue":"6","key":"pcbi.1012813.ref104","article-title":"Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues","volume":"11","author":"KR McCarthy","year":"2020","journal-title":"MBio [Internet]"},{"issue":"2","key":"pcbi.1012813.ref105","doi-asserted-by":"crossref","first-page":"274","DOI":"10.3390\/v15020274","article-title":"Unique Structure and Distinctive Properties of the Ancient and Ubiquitous Gamma-Type Envelope Glycoprotein","volume":"15","author":"V Hogan","year":"2023","journal-title":"Viruses"},{"issue":"4","key":"pcbi.1012813.ref106","doi-asserted-by":"crossref","first-page":"e0149521","DOI":"10.1128\/mbio.01495-21","article-title":"Ancient gene capture and recent gene loss shape the evolution of orthopoxvirus-host interaction genes","volume":"12","author":"TG 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and disease relevance","volume":"8","author":"Y Yang","year":"2023","journal-title":"Signal Transduct Target Ther"},{"issue":"6598","key":"pcbi.1012813.ref114","doi-asserted-by":"crossref","first-page":"eabm9506","DOI":"10.1126\/science.abm9506","article-title":"AI-based structure prediction empowers integrative structural analysis of human nuclear pores","volume":"376","author":"S Mosalaganti","year":"2022","journal-title":"Science"},{"issue":"1","key":"pcbi.1012813.ref115","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/S0378-1119(99)00122-5","article-title":"Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins","volume":"232","author":"PA Kenny","year":"1999","journal-title":"Gene"},{"issue":"2","key":"pcbi.1012813.ref116","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.neuron.2012.02.029","article-title":"Complementary chimeric isoforms reveal Dscam1 binding specificity in vivo","volume":"74","author":"W Wu","year":"2012","journal-title":"Neuron"},{"issue":"5","key":"pcbi.1012813.ref117","doi-asserted-by":"crossref","first-page":"e1501118","DOI":"10.1126\/sciadv.1501118","article-title":"Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition","volume":"2","author":"SA Li","year":"2016","journal-title":"Sci Adv"},{"issue":"2","key":"pcbi.1012813.ref118","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.str.2010.12.014","article-title":"Structural model and trans-interaction of the entire ectodomain of the olfactory cell adhesion molecule","volume":"19","author":"N Kulahin","year":"2011","journal-title":"Structure"},{"issue":"9","key":"pcbi.1012813.ref119","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1038\/nsmb.2366","article-title":"Nectin ectodomain structures reveal a canonical adhesive interface","volume":"19","author":"OJ Harrison","year":"2012","journal-title":"Nat Struct Mol 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Lesk","year":"1988","journal-title":"Nature"},{"key":"pcbi.1012813.ref127","doi-asserted-by":"crossref","first-page":"675655","DOI":"10.3389\/fimmu.2021.675655","article-title":"Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics","volume":"12","author":"ML Fern\u00e1ndez-Quintero","year":"2021","journal-title":"Front Immunol"},{"issue":"4","key":"pcbi.1012813.ref128","doi-asserted-by":"crossref","first-page":"67","DOI":"10.3390\/antib12040067","article-title":"Structure and dynamics guiding design of antibody therapeutics and vaccines","volume":"12","author":"ML Fern\u00e1ndez-Quintero","year":"2023","journal-title":"Antibodies"},{"issue":"1","key":"pcbi.1012813.ref129","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1002\/prot.22319","article-title":"Conserved amino acid networks involved in antibody variable domain interactions","volume":"76","author":"N Wang","year":"2009","journal-title":"Proteins"},{"key":"pcbi.1012813.ref130","doi-asserted-by":"crossref","first-page":"812750","DOI":"10.3389\/fmolb.2022.812750","article-title":"Comparing antibody interfaces to inform rational design of new antibody formats","volume":"9","author":"ML Fern\u00e1ndez-Quintero","year":"2022","journal-title":"Front Mol Biosci"},{"key":"pcbi.1012813.ref131","doi-asserted-by":"crossref","first-page":"811632","DOI":"10.3389\/fimmu.2021.811632","article-title":"Structural Basis of antibody conformation and stability modulation by framework somatic hypermutation","volume":"12","author":"Z Sheng","year":"2022","journal-title":"Front Immunol"},{"issue":"9","key":"pcbi.1012813.ref132","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.3390\/biom11091290","article-title":"Topological and structural plasticity of the single ig fold and the double ig fold present in CD19","volume":"11","author":"P Youkharibache","year":"2021","journal-title":"Biomolecules"},{"issue":"4","key":"pcbi.1012813.ref133","doi-asserted-by":"crossref","first-page":"710","DOI":"10.3390\/cryst13040710","article-title":"Crystal structure of a chimeric antigen receptor (CAR) scFv Domain rearrangement forming a VL-VL Dimer","volume":"13","author":"J Cheung","year":"2023","journal-title":"Crystals"},{"issue":"14","key":"pcbi.1012813.ref134","doi-asserted-by":"crossref","first-page":"5399","DOI":"10.1073\/pnas.1120606109","article-title":"Structure of TIGIT immunoreceptor bound to poliovirus receptor reveals a cell-cell adhesion and signaling mechanism that requires cis-trans receptor clustering","volume":"109","author":"KF Stengel","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1012813.ref135","doi-asserted-by":"crossref","DOI":"10.1016\/j.str.2018.10.023","article-title":"Structural basis for CD96 immune receptor recognition of nectin-like Protein-5, 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