{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_XL3_CSMs.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_CenpA_XL2_CSMs.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_CenpA_XL1_CSMs.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_XL2_CSMs.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_XL1_CSMs.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_CenpA_XL3_CSMs.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_XL2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_CenpA_XL3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_CenpA_XL1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_XL3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_CenpA_XL2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/20190404_L1_Ag6_fasci001_SA_CCAN_XL1.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/CCAN_databse.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013769/CCAN_CenpA_database.fasta"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["A.J.R.Heck@uu.nl"],"submitter":["Domenico Fasci"],"technology_type":["Mass Spectrometry","Chemical cross-linking coupled with mass spectrometry proteomics"],"software":["Not available"],"submitter_keywords":["Cryo-em structure","S.cerevisiae","Xl-ms","Inner kinetochore complex"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD013769"],"sample_protocol":["The CCAN and CCAN-CenpA complexes were recombinantly expressed and purified from insect cells. After reconstitution the final complexes were isolated through multiple chromatography rounds. The samples were cross-linked using the DSSO cross-linker and processed using a standard bottom-up proteomics sample preparation. The samples were analysed by LC-MS/MS with a MS2/MS3 acquisition strategy."],"repository":["Pride"],"quantification_method":["Not available"],"modification":["iodoacetamide derivatized residue","monohydroxylated residue"],"data_protocol":["The data was analysed with Proteome Discoverer 2.3 with the XlinkX nodes integrated."],"omics_type":["Proteomics"],"labhead":["Albert J.R. Heck"],"instrument_platform":["Orbitrap Fusion Lumos"],"labhead_affiliation":["Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"submission_type":["PARTIAL"],"species":["Saccharomyces Cerevisiae (baker's Yeast)"],"publication":["31578520 Yan K, Yang J, Zhang Z, McLaughlin SH, Chang L, Fasci D, Ehrenhofer-Murray AE, Heck AJR, Barford D. Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Nature. 2019 10.1038/s41586-019-1609-1"],"submitter_mail":["d.fasci@uu.nl"],"curator_keywords":["Epic-xs"],"submitter_affiliation":["Utrecht University"],"submitter_country":["Netherlands"],"pubmed_abstract":["In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes1,2, function to connect centromeric chromatin to microtubules of the mitotic spindle3,4. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules5,6. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-ANuc), each of which is perfectly centred on its cognate centromere7-9. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-ANuc). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-ANuc to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-ANuc are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-ANuc. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation."],"pubmed_title":["Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome."],"pubmed_authors":["Yan Kaige K, Yang Jing J, Zhang Ziguo Z, McLaughlin Stephen H SH, Chang Leifu L, Fasci Domenico D, Ehrenhofer-Murray Ann E AE, Heck Albert J R AJR, Barford David D"],"sample_synonyms":["CG13329, CenH3[CID], CenH3[Cid], liquid chromatography tandem mass spectroscopy, LC-MS2, BcDNA:RE21270, LCMSMS, CenH3, CenH3/CID, CENP-A/Cid, CENP-A/CID, Peptidomics, MS/MS, CENPA, MS2, Cid[Mel], LC-MS/MS, E430039A18Rik, DmelCG13329, cenH3, CD156a, CENP-A, Insect, Cell, CD156, CENP-C, CID, Cid, LC-MS-MS, CenpA, LC/MS/MS, MS3., liquid chromatography-tandem mass spectroscopy, LC-MSMS, Cenp-A, liquid chromatography tandem mass spectrometry, Insects, Chromatographies, CenpA/CID, tandem MS, cenpA, CID/CENP-A"],"pubmed_title_synonyms":["condensed nuclear chromosome kinetochore, condensed chromosome kinetochore, CenH3 containing nucleosome, centromere specific nucleosome., Kinetochore, CNP-T-W-S-X complex, NMS complex, centromere-specific nucleosome, centromeric nucleosome, CENP-S-T-W-X, conformation, relational structural quality"],"data_synonyms":["data."],"description_synonyms":["CG13329, CenH3[CID], CenH3[Cid], Budding Yeasts, Saccharomycetale, Yeasts, Yeast, BcDNA:RE21270, CenH3, CenH3/CID, CENP-A/Cid, CENP-A/CID, conformation, CENPA, Cid[Mel], nuclear nucleosome, cytoplasmic nucleosome, DmelCG13329, cenH3, organisation., CENP-A, CENP-C, CID, Cid, CenpA, Endomycetale, Budding Yeast, Endomycopses, Endomycopsis, Cenp-A, associated, CenpA/CID, relational structural quality, Endomycetales, Budding, cenpA, CID/CENP-A"],"pubmed_abstract_synonyms":["INSDC_feature:centromere, Chromosome Segregations, lop13, FON1, PNT-P1, Cid[Mel], DmelCG17077, Mbp1, Phases, EY3-1, protein, Pnt, sci, FLORAL ORGAN NUMBER 1, CENP-A, CENP-C, CENP-N, Endomycetale, protein polypeptide chains, Mitotic M, Polynucleosome, CENP-L, png, chromosome number anomaly, concavities, SUP, AA959943, HOW, How, D-ets-2, 3520, cenp-n, protein aggregate, myd, Chromatins, SREBP2gc, l(3)j5D5, Pnt-P1, Aneuploid Cell, CG13329, 24B, C16orf60, thymus nucleic acid, ostium, BcDNA:RE21270, M Phases, AI608257, Genomes, Aneuploid, inner kinetochore of condensed chromosome, N, Bdr, nuclear nucleosome, stru, Mbp-1, proteins, Baker, l(3)S053606, SREBP2, Eucarya, Super protein, Saccharomyces uvarum var. melibiosus, CG10293, sp, eucaryotes, SNAP-25, condensed chromosome inner kinetochore, Acts, outer kinetochore of condensed nuclear chromosome, centromere, l(3)j5B5, Budding Yeast, centric region, Endomycopses, Saccharomyces capensis, chromosome scaffold, Cenp-A, Baker's, Double-Stranded DNA, Mycoderma cerevisiae, Segregations, deoxyribonucleic acids, DNAn, brewer's yeast, associated, SIMPLE, ostia, Budding, nuclear chromatin, Base Pairings, Budding Yeasts, ICEN32, Acta-2, Saccharomycetale, 0904/17, common ribonucleoside residue, dJ383J4.3, Meiotic M Phase, gyltl1b-b, Actsk-1, D-Ets-2, ets94F, 0123/09, Double-Stranded, foramina, Cid, CID, (Deoxyribonucleotide)n+m, Baker's Yeasts, bHLHd2, Nucleosome, Saccharomyces diastaticus, inner kinetochore of condensed nuclear chromosome, SZ1, MDDGA6, PIG7, mKIAA0609, fossae, GENA70, outer kinetochore plate, desoxyribose nucleic acid, Microtubule, Meiotic M Phases, cenpA, Dinucleosome, fg, Yeasts, Yeast, pntP2, gyltl1b, Pointed-P1, Mitoses, CenH3/CID, CENP-A/Cid, CENP-A/CID, CENPA, mdc1d, Ets94F, Eukarya, expanded, Kinetochore, depressions, Interphase centromere complex protein 32, Interphase centromere complex protein 33, ptd, CALNUC, MDC1D, PntP2, enr, cenpn, Chromosome, enlarged, PntP1, Endomycopsis, E(E2F)3D, Cells, ds DNA, canonical ribonucleoside residues, anon-EST:Liang-2.39, Mitotic, PNTP2, DNA, PNTP1, Brewer's Yeast, Endomycetales, FLORAL DEFECTIVE 10, big, meiosis, cytoplasmic chromatin, 0998/12, Segregation, DNS, (Deoxyribonucleotide)n, condensed nuclear chromosome outer kinetochore, conformation, RP3-383J4.1, P62, ETS2, Ets2, Eukaryotes, Brewer's, baker's yeast, SUPERMAN, protein-containing complex, common ribonucleoside residues, Saccharomyces italicus, froggy, Deoxyribonucleic acids, Gyltl1a, CenpA, Aneuploidies, large, DMPOINT1A, pntegfr, 0608/07, polypeptide chain, Deoxyribonucleic Acid, pericentric region, CenH3[Cid], CenH3[CID], C1orf155, Centromeres, SREBP-2, l(3)s2612, pointed-RC, fossa, MDDGB6, ligand, Chromosome., DmelCG13329, Double Stranded, Meioses, Deoxyribonucleic acid, concavity, EK3-2, NUC, Nuc, condensed chromosome outer kinetochore, S. cerevisiae, Aneuploid Cells, BPFD#36, l(3)07825, Mif1, Meiotic, S cerevisiae, chromosome transmission, Candida robusta, Base Pair, great, DmelCG10293, CG17077, (Deoxyribonucleotide)m, relational structural quality, chromosome division, l(3)j1B7, nuc, TP53I7, Aneuploids, inner centromere core complex, data, Ets, foramen, Eukaryote, Saccharomyces cerevisiae 'var. diastaticus', protein complex, clone 2.39, DNAn+1, condensed nuclear chromosome inner kinetochore, cenH3, Eukaryotas, Synaptosomal-associated 25 kDa protein, function, qkr, l(3)S090417, Cell, eukaryotes, Centromere protein A, native protein, outer kinetochore of condensed chromosome, natural protein, mitosis, KH93F, Protein, BM039, Mitotic M Phase, Polynucleosomes, Vertebrate, ds-DNA, M Phase, pnt-P1, pnt-P2, centromere complex, l(3)s118306, cell surface groove, who, Saccharomyces oviformis, Phase, Base Pairs, furrow, Meiotic M, groove, CenH3, cytoplasmic nucleosome, FLO10, Who/How, HERP, Centromere autoantigen A, Dinucleosomes, Eukaryotae, Ets58AB, chromosome, opening, Mitotic M Phases, Desoxyribonukleinsaeure, qkr[93F], standard ribonucleoside residues, Eucaryotae, Baker's Yeast, CenpA/CID, depression, POINT, inner kinetochore plate, Baker Yeast, CID/CENP-A, CG8705"],"name_synonyms":["Mass Spectrum Analysis, CenH3[Cid], CG13329, CenH3[CID], Mass Spectrum, cenpA., BcDNA:RE21270, CenH3, CenH3/CID, Analyses, CENP-A/Cid, CENP-A/CID, CENPA, Cid[Mel], Spectrometry, DmelCG13329, cenH3, Spectrum Analyses, Centromere autoantigen A, Spectrum Analysis, CENP-A, Cid, CENP-C, CID, Spectroscopy, Centromere protein A, CenpA, Cenp-A, Mass, Analysis, CenpA/CID, Mass Spectrum Analyses, Mass Spectroscopy, CID/CENP-A"],"additional_accession":[]},"is_claimable":false,"name":"Cross-linking mass spectrometry of the CCAN and CCAN-Cenp-A complexes","description":"Here we performed a cross-linking mass spectrometry analysis of the inner kinethocore complex CCAN and of the complex associated with a CenpA-nucleosome (CCAN-CenpA)from budding yeast. 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