{"title":"利用 checkMySequence 验证蛋白质晶体结构模型中的序列配准。","authors":"Grzegorz Chojnowski","doi":"10.1107/S2059798323003765","DOIUrl":null,"url":null,"abstract":"<p><p>Sequence-register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication, it was shown that register shifts in cryo-EM models of proteins can be detected using a systematic reassignment of short model fragments to the target sequence. Here, it is shown that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias-corrected electron-density maps (2mF<sub>o</sub> - DF<sub>c</sub>). Five register-shift errors in models deposited in the PDB detected using this method are described in detail.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 7","pages":"559-568"},"PeriodicalIF":2.6000,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306063/pdf/","citationCount":"0","resultStr":"{\"title\":\"Sequence-assignment validation in protein crystal structure models with checkMySequence.\",\"authors\":\"Grzegorz Chojnowski\",\"doi\":\"10.1107/S2059798323003765\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Sequence-register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication, it was shown that register shifts in cryo-EM models of proteins can be detected using a systematic reassignment of short model fragments to the target sequence. Here, it is shown that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias-corrected electron-density maps (2mF<sub>o</sub> - DF<sub>c</sub>). Five register-shift errors in models deposited in the PDB detected using this method are described in detail.</p>\",\"PeriodicalId\":7116,\"journal\":{\"name\":\"Acta Crystallographica. Section D, Structural Biology\",\"volume\":\"79 Pt 7\",\"pages\":\"559-568\"},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2023-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306063/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Acta Crystallographica. Section D, Structural Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1107/S2059798323003765\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2023/6/14 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Acta Crystallographica. Section D, Structural Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1107/S2059798323003765","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/6/14 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
Sequence-assignment validation in protein crystal structure models with checkMySequence.
Sequence-register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication, it was shown that register shifts in cryo-EM models of proteins can be detected using a systematic reassignment of short model fragments to the target sequence. Here, it is shown that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias-corrected electron-density maps (2mFo - DFc). Five register-shift errors in models deposited in the PDB detected using this method are described in detail.
期刊介绍:
Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them.
Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged.
Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.