Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome

2026-07-29 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-11-18 2026-05-20 2026-05-20 2026-07-29 Medical Research Council (MRC, United Kingdom) MC_UP_120 United Kingdom Cancer Research UK C576/A25675 United Kingdom Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome Yu C Barford D Centromeres, Kinetochores, CELL CYCLE Yu C Muir KW Yang J Zhang Z McLaughlin SH Barford D Models for the architecture of the human inner kinetochore on centromeric alpha-satellite CENP-A nucleosome arrays. Nat Commun UK 17 2026 42120391 doi:10.1038/s41467-026-72856-0 2041-1723 EMD-55755 focused EM volume EMD-55756 focused EM volume EMD-56612 consensus EM volume 9tay FULLOVERLAP EMDB EMD-55755 focused EM volume EMDB EMD-55756 focused EM volume EMDB EMD-55759 associated EM volume

EMDB EMD-56612 consensus EM volume Human inner kinetochore CCAN bound to a di-CENP-A nucleosome Human inner kinetochore CCAN bound to a di-CENP-A nucleosome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 22 Homo sapiens Centromere protein H Homo sapiens 0.028520940999999998 1 Trichoplusia ni LEVO MEEQPQMQDADEPADSGGEGRAGGPPQVAGAQAACSEDRMTLLLRLRAQTKQQLLEYKSMVDASEEKTPEQIMQEKQIEA KIEDLENEIEEVKVAFEIKKLALDRMRLSTALKKNLEKISRQSSVLMDNMKHLLELNKLIMKSQQESWDLEEKLLDIRKK RLQLKQASESKLLEIQTEKNKQKIDLDSMENSERIKIIRQNLQMEIKITTVIQHVFQNLILGSKVNWAEDPALKEIVLQL EKNVDMM Q9H3R5 Centromere protein I Homo sapiens 0.087615031 1 Trichoplusia ni LEVO MSPQKRVKNVQAQNRTSQGSSSFQTTLSAWKVKQDPSNSKNISKHGQNNPVGDYEHADDQAEEDALQMAVGYFEKGPIKA SQNKDKTLEKHLKTVENVAWKNGLASEEIDILLNIALSGKFGNAVNTRILKCMIPATVISEDSVVKAVSWLCVGKCSGST KVLFYRWLVAMFDFIDRKEQINLLYGFFFASLQDDALCPYVCHLLYLLTKKENVKPFRVRKLLDLQAKMGMQPHLQALLS LYKFFAPALISVSLPVRKKIYFKNSENLWKTALLAVKQRNRGPSPEPLKLMLGPANVRPLKRKWNSLSVIPVLNSSSYTK ECGKKEMSLSDCLNRSGSFPLEQLQSFPQLLQNIHCLELPSQMGSVLNNSLLLHYINCVRDEPVLLRFYYWLSQTLQEEC IWYKVNNYEHGKEFTNFLDTIIRAECFLQEGFYSCEAFLYKSLPLWDGLCCRSQFLQLVSWIPFSSFSEVKPLLFDHLAQ LFFTSTIYFKCSVLQSLKELLQNWLLWLSMDIHMKPVTNSPLETTLGGSMNSVSKLIHYVGWLSTTAMRLESNNTFLLHF ILDFYEKVCDIYINYNLPLVVLFPPGIFYSALLSLDTSILNQLCFIMHRYRKNLTAAKKNELVQKTKSEFNFSSKTYQEF NHYLTSMVGCLWTSKPFGKGIYIDPEILEKTGVAEYKNSLNVVHHPSFLSYAVSFLLQESPEERTVNVSSIRGKKWSWYL DYLFSQGLQGLKLFIRSSVHHSSIPRAEGINCNNQYENLYFQ Q92674 Centromere protein K Homo sapiens 0.03169607 1 Trichoplusia ni LEVO MNQEDLDPDSTTDVGDVTNTEEELIRECEEMWKDMEECQNKLSLIGTETLTDSNAQLSLLIMQVKCLTAELSQWQKKTPE TIPLTEDVLITLGKEEFQKLRQDLEMVLSTKESKNEKLKEDLEREQRWLDEQQQIMESLNVLHSELKNKVETFSESRIFN ELKTKMLNIKEYKEKLLSTLGEFLEDHFPLPDRSVKKKKKNIQESSVNLITLHEMLEILINRLFDVPHDPYVKISDSFWP PYVELLLRNGIALRHPEDPTRIRLEAFHQ Q9BS16 Centromere protein L Homo sapiens 0.039364016 1 Trichoplusia ni LEVO GPLGMDSYSAPESTPSASSRPEDYFIGATPLQKRLESVRKQSSFILTPPRRKIPQCSQLQEDVDPQKVAFLLHKQWTLYS LTPLYKFSYSNLKEYSRLLNAFIVAEKQKGLAVEVGEDFNIKVIFSTLLGMKGTQRDPEAFLVQIVSKSQLPSENREGKV LWTGWFCCVFGDSLLETVSEDFTCLPLFLANGAESNTAIIGTWFQKTFDCYFSPLAINAFNLSWMAAMWTACKMDHYVAT TEFLWSVPCSPQSLDISFAIHPEDAKALWDSVHKTPGEVTQEEVDLFMDCLYSHFHRHFKIHLSATRLVRVSTSVASAHT DGKIKILCHKYLIGVLAYLTELAIFQIE Q8N0S6 Centromere protein M Homo sapiens 0.019761945 1 Trichoplusia ni LEVO MSVLRPLDKLPGLNTATILLVGTEDALLQQLADSMLKEDCASELKVHLAKSLPLPSSVNRPRIDLIVFVVNLHSKYSLQN TEESLRHVDASFFLGKVCFLATGAGRESHCSIHRHTVVKLAHTYQSPLLYCDLEVEGFRATMAQRLVRVLQICAGHVPGV SALNLLSLLRSSEGPSLEDL Q9NSP4 Centromere protein N Homo sapiens 0.040541641 1 Trichoplusia ni LEVO MDETVAEFIKRTILKIPMNELTTILKAWDFLSENQLQTVNFRQRKESVVQHLIHLCEEKRASISDAALLDIIYMQFHQHQ KVWEVFQMSKGPGEDVDLFDMKQFKNSFKKILQRALKNVTVSFRETEENAVWIRIAWGTQYTKPNQYKPTYVVYYSQTPY AFTSSSMLRRNTPLLGQALTIASKHHQIVKMDLRSRYLDSLKAIVFKQYNQTFETHNSTTPLQERSLGLDINMDSRIIHE NIVEKERVQRITQETFGDYPQPQLEFAQYKLETKFKSGLNGSILAERKEPLRCLIKFSSPHLLEALKSLAPAGIADAPLS PLLTCIPNKRMNYFKIRDKSDLEVLFQ Q96H22 Centromere protein O Homo sapiens 0.033830637000000004 1 Trichoplusia ni LEVO MEQANPLRPDGESKGGVLAHLERLETQVSRSRKQSEELQSVQAQEGALGTKIHKLRRLRDELRAVVRHRRASVKACIANV EPNQTVEINEQEALEEKLENVKAILQAYHFTGLSGKLTSRGVCVCISTAFEGNLLDSYFVDLVIQKPLRIHHHSVPVFIP LEEIAAKYLQTNIQHFLFSLCEYLNAYSGRKYQADRLQSDFAALLTGPLQRNPLCNLLSFTYKLDPGGQSFPFCARLLYK DLTATLPTDVTVTCQGVEVLSTSWEEQRASHETLFCTKPLHQVFASFTRKGEKLDMSLVS Q9BU64 Centromere protein Q Homo sapiens 0.024634549 1 Trichoplusia ni LEVO MTKHTNLKHGKTAASKRKTWQPLSKSTRDHLQTMMESVIMTILSNSIKEKEEIQYHLNFLKKRLLQQCETLKVPPKKMED LTNVSSLLNMERARDKANEEGLALLQEEIDKMVETTELMTGNIQSLKNKIQILASEVEEEEERVKQMHQINSSGVLSLPE LSQKTLKAPTLQKEILALIPNQNALLKDLDILHNSSQMKSMSTFIEEAYKKLDAS Q7L2Z9 Centromere protein U Homo sapiens 0.024484872999999997 1 Trichoplusia ni LEVO MKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKEQFIKMLKESQMLTNLKRKNAKMISDIEKKRQRMIE VQDELLRLEPQLKQLQTKYDELKERKSSLRNAAYFLSNLKQLYQDYSDVQAQEPNVKETYDSSSLPALLFKARTLLGAES HLRNINHQLEKLLDQGENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK Q71F23 Centromere protein P Homo sapiens 0.033210949 1 Trichoplusia ni LEVO MDAELAEVRALQAEIAALRRACEDPPAPWEEKSRVQKSFQAIHQFNLEGWKSSKDLKNQLGHLESELSFLSTLTGINIRN HSKQTEDLTSTEMTEKSIRKVLQRHRLSGNCHMVTFQLEFQILEIQNKERLSSAVTDLNIIMEPTECSELSEFVSRAEER KDLFMFFRSLHFFVEWFEYRKRTFKHLKEKYPDAVYLSEGPSSCSMGIRSASRPGFELVIVWRIQIDEDGKVFPKLDLLT KVPQRALELDKNRAIETAPLSFRTLVGLLGIEAALESLIKSLCAEENN Q6IPU0 Centromere protein R Homo sapiens 0.020228297 1 Trichoplusia ni LEVO MPVKRSLKLDGLLEENSFDPSKITRKKSVITYSPTTGTCQMSLFASPTSSEEQKHRNGLSNEKRKKLNHPSLTESKESTT KDNDEFMMLLSKVEKLSEEIMEIMQNLSSIQALEGSRELENLIGISCASHFLKREMQKTKELMTKVNKQKLFEKSTGLPH KASRHLDSYEFLKAILN Q13352 Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T Homo sapiens 0.08406767999999999 1 Trichoplusia ni LEVO MSYYHHHHHHDYDIPTTENLYFQGMDKDCEMKRTTLDSPLGKLELSGCEQGLHRIIFLGKGTSAADAVEVPAPAAVLGGP EPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAGNPAATAAVKTALSG NPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKPGLGSDLEVLFQGPMADHNPDSDSTPRTLLRRVLDTAD PRTPRRPRSARAGARRALLETASPRKLSGQTRTIARGRSHGARSVGRSAHIQASGHLEEQTPRTLLKNILLTAPESSILM PESVVKPVPAPQAVQPSRQESSCGSLELQLPELEPPTTLAPGLLAPGRRKQRLRLSVFQQGVDQGLSLSQEPQGNADASS LTRSLNLTFATPLQPQSVQRPGLARRPPARRAVDVGAFLRDLRDTSLAPPNIVLEDTQPFSQPMVGSPNVYHSLPCTPHT GAEDAEQAAGRKTQSSGPGLQKNSPGKPAQFLAGEAEEVNAFALGFLSTSSGVSGEDEVEPLHDGVEEAEKKMEEEGVSV SEMEATGAQGPSRVEEAEGHTEVTEAEGSQGTAEADGPGASSGDEDASGRAASPESASSTPESLQARRHHQFLEPAPAPG AAVLSSEPAEPLLVRHPPRPRTTGPRPRQDPHKAGLSHYVKLFSFYAKMPMERKALEMVEKCLDKYFQHLCDDLEVFAAH AGRKTVKPEDLELLMRRQGLVTDQVSLHVLVERHLPLEYRQLLIPCAYSGNSVFPAQ P16455 Q96BT3 2.1.1.63 Centromere protein W Homo sapiens 0.010087236000000001 1 Trichoplusia ni LEVO MALSTIVSQRKQIKRKAPRGFLKRVFKRKKPQLRLEKSGDLLVHLNCLLFVHRLAEESRTNACASKCRVINKEHVLAAAK VILKKSRG Q5EE01 Centromere protein S Homo sapiens 0.015917874999999998 1 Trichoplusia ni LEVO MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTE DVKLLARRSNSLLKYITDKSEEIAQINLERKAQKKKKSEDGSKNSRQPAEAGVVESEN Q8N2Z9 Centromere protein X Homo sapiens 0.008972415000000001 1 Trichoplusia ni LEVO MEGAGAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQLLLD F A8MT69 Histone H3-like centromeric protein A Homo sapiens 0.016023629999999997 4 Escherichia coli LEVO MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTR GVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG P49450 Histone H4 Homo sapiens 0.011394426 4 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A type 1-C Homo sapiens 0.016666333999999998 4 Escherichia coli LEVO MGSSHHHHHHSPGLEVLFQGPRGMSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLE YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK Q93077 Histone H2B type 1-C/E/F/G/I Homo sapiens 0.013937212999999999 4 Escherichia coli LEVO MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK P62807 DNA (318-MER) Homo sapiens 0.09981058599999999 1 (DA)(DT)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DT)(DA)(DT)(DC)(DT)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC)(DC)(DT)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG)(DT)(DG) (DG)(DA)(DC)(DA)(DT)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DG)(DC)(DC)(DT)(DT)(DC)(DG)(DT)(DT)(DG)(DG)(DA)(DA)(DA)(DC)(DG)(DG)(DG)(DA)(DA) (DT)(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DG) (DA)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DT)(DT)(DG)(DT)(DA)(DG)(DT) (DA)(DT)(DC)(DT)(DG)(DG)(DA)(DA)(DT)(DT)(DG)(DG)(DA)(DC)(DA)(DT)(DT)(DT)(DG)(DG) (DA)(DG)(DA)(DT) DNA DNA (318-MER) Homo sapiens 0.10029084399999999 1 (DA)(DT)(DC)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DC)(DC)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DG)(DA)(DT)(DA)(DC)(DT)(DA)(DC)(DA)(DA)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DT)(DC)(DT)(DA)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DA) (DC)(DA)(DT)(DA)(DT)(DT)(DC)(DC)(DC)(DG)(DT)(DT)(DT)(DC)(DC)(DA)(DA)(DC)(DG)(DA) (DA)(DG)(DG)(DC)(DC)(DA)(DC)(DA)(DA)(DA)(DG)(DT)(DG)(DC)(DT)(DC)(DC)(DG)(DA)(DA) (DT)(DG)(DT)(DC)(DC)(DA)(DC)(DT)(DT)(DG)(DC)(DA)(DG)(DA)(DT)(DA)(DC)(DT)(DA)(DC) (DA)(DA)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DT)(DC)(DT)(DA)(DG)(DT) (DT)(DT)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DA)(DG)(DA)(DT)(DA)(DT)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DT) DNA scFv Mus musculus 0.029161339999999997 4 Escherichia coli LEVO MMKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQTPRQGLEWIGYIYPYNAGTK YNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKSSRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIK MTQSPSSMHASLGERVTITCKASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDT ATYYCLQHGESPYTFGSGTKLEIKRA singleParticle particle 7.4 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 BIOQUANTUM (6k x 4k) 40.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 15.5 FSC 0.143 CUT-OFF RELION 15057 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION emd_55759.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 371.19998 371.19998 371.19998 90.0 90.0 90.0 X Y Z -0.0013963185 0.0059859743 0.000103226914 0.00045781521 0.928 0.928 0.928 0.0015 AUTHOR ::::EMDATABANK.org::::EMD-55759::::