6TM5: Anaphase-promoting complex/Cyclosome

Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution. Determined by electron microscopy at 3.9 Å resolution. Released 19 Feb 2020.

Method
Electron microscopy
Resolution
3.9 Å
Organism
Homo sapiens
Chains
22
Atoms
63,885
Mol. weight
1277.49 kDa
Ligands
ZN
Released
19 Feb 2020

Explore 6TM5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TM5 contains 429 α-helices and 119 β-strands across 19 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 68 helices, 52 β-strands

ElementResiduesLengthSheet
β-strand1311
β-strand16-2052
α-helix23-286
β-strand73-7863
β-strand90-9563
β-strand99-10353
β-strand113-11863
β-strand12314
β-strand127-12825
β-strand150-15455
β-strand15514
β-strand159-16355
β-strand168-17145
β-strand180-18346
β-strand186-18946
β-strand211-21336
α-helix219-2202
β-strand221-22226
β-strand224-22527
β-strand237-23827
β-strand244-24968
β-strand256-26058
β-strand268-27257
β-strand408-41367
β-strand430-43239
β-strand440-44569
β-strand452-45989
α-helix4651
β-strand466-47499
β-strand478-482510
β-strand487-492610
β-strand496-500510
β-strand505-507310
β-strand51011
β-strand584-59182
β-strand594-59962
β-strand604-60852
α-helix609-6113
α-helix616-62813
α-helix631-64616
α-helix656-66510
α-helix674-6763
α-helix705-7128
α-helix714-7218
α-helix759-77618
α-helix783-79715
α-helix801-8099
α-helix811-8144
α-helix844-8529
α-helix868-88013
α-helix928-9369
α-helix941-9444
α-helix949-96416
α-helix972-9776
α-helix981-99111
α-helix1021-10277
α-helix1033-10419
β-strand1047-1048211
α-helix1059-107719
α-helix1080-10878
β-strand1092112
α-helix1093-10953
α-helix1101-11044
β-strand1108-1111411
β-strand1116-1119411
α-helix1133-114513
β-strand1147112
α-helix1148-11492
α-helix1169-118113
α-helix1194-11996
α-helix1202-121615
α-helix1222-123110
α-helix1247-126115
α-helix1267-127711
α-helix1291-130616
α-helix1321-133010
β-strand1352-1353213
α-helix1360-137415
α-helix1381-13855
α-helix1396-13983
α-helix1401-141414
α-helix1423-14275
α-helix1432-14365
α-helix1457-147418
α-helix1482-150019
α-helix1504-15074
α-helix1509-152618
α-helix1533-154412
α-helix1552-156514
α-helix1567-15693
β-strand1572114
α-helix1580-15878
α-helix1604-16129
β-strand1616114
β-strand1618115
β-strand1620116
β-strand1622-1623217
α-helix1624-16263
β-strand1628-1629217
β-strand1633-1638618
β-strand1650-1652318
β-strand1656115
β-strand1663-1668618
α-helix1686-16905
β-strand1696116
β-strand1699117
α-helix1735-17395
α-helix1745-17506
α-helix1751-17555
α-helix1765-178016
α-helix1787-180115
α-helix1809-182012
α-helix1824-18274
α-helix1845-186218
α-helix1865-18728
α-helix1876-18783
α-helix1881-18888
α-helix1889-18935
α-helix1913-19208
α-helix1925-19317
Chain B: 3 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand3-10819
β-strand13120
α-helix33-342
α-helix41-433
β-strand46-48321
β-strand54-56321
α-helix57-6711
Chain C: 31 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix29-4618
α-helix49-6113
α-helix71-755
α-helix78-9417
α-helix99-1068
α-helix112-13625
α-helix151-16313
α-helix170-18112
α-helix185-19814
α-helix203-2108
α-helix216-2216
α-helix229-24012
α-helix244-25613
α-helix259-2613
α-helix264-27512
α-helix280-29213
α-helix300-30910
α-helix313-32614
α-helix331-34414
α-helix347-36014
α-helix368-37710
α-helix381-39414
α-helix399-41113
α-helix415-42814
α-helix434-44512
α-helix449-46113
α-helix469-47911
α-helix483-49816
α-helix510-52314
α-helix526-53813
α-helix545-55612
Chain D: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-113
α-helix27-4519
Chain E: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix53-8836
α-helix89-913
α-helix93-953
α-helix97-982
α-helix99-1024
Chain F: 30 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-1812
α-helix21-3414
α-helix38-5114
α-helix54-629
α-helix69-8113
α-helix86-927
α-helix105-1106
α-helix113-12715
α-helix131-14414
α-helix150-1589
α-helix161-1633
α-helix164-1674
α-helix456-47722
α-helix481-4899
α-helix493-4964
α-helix499-51113
α-helix515-52915
α-helix536-54510
α-helix549-56214
α-helix567-57812
α-helix583-59614
α-helix602-61211
α-helix619-63012
α-helix635-64713
α-helix651-66414
α-helix668-68114
α-helix694-6985
α-helix703-71412
α-helix719-73012
α-helix737-75014
Chain G: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix4-96
α-helix13-164
α-helix18-225
Chain H: 30 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-1610
α-helix21-3515
α-helix38-5013
α-helix54-6310
α-helix69-8113
α-helix85-928
α-helix103-1108
α-helix111-1133
α-helix114-12714
α-helix131-14414
α-helix150-1578
α-helix165-1739
α-helix452-47726
α-helix481-4888
α-helix499-51214
α-helix515-52814
α-helix536-54510
α-helix549-56214
α-helix567-57913
α-helix583-59513
α-helix602-61312
α-helix617-63014
α-helix635-64814
α-helix651-66414
α-helix669-68214
α-helix685-69814
α-helix704-71512
α-helix719-73214
α-helix737-75014
α-helix753-76614

11 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Anaphase-promoting complex subunit 1Aprotein1944Homo sapiensQ9H1A4 (AlphaFold model)
Anaphase-promoting complex subunit 11Bprotein84Homo sapiensQ9NYG5 (AlphaFold model)
Cell division cycle protein 23 homologC, Pprotein597Homo sapiensQ9UJX2 (AlphaFold model)
Anaphase-promoting complex subunit 15Dprotein121Homo sapiensP60006 (AlphaFold model)
Anaphase-promoting complex subunit 16Eprotein110Homo sapiensQ96DE5
Cell division cycle protein 27 homologF, Hprotein824Homo sapiensP30260
Anaphase-promoting complex subunit CDC26G, Wprotein85Homo sapiensQ8NHZ8
Anaphase-promoting complex subunit 4Iprotein808Homo sapiensQ9UJX5
Cell division cycle protein 16 homologJ, Kprotein620Homo sapiensQ13042
Anaphase-promoting complex subunit 10Lprotein185Homo sapiensQ9UM13
Anaphase-promoting complex subunit 13Mprotein74Homo sapiensQ9BS18
Anaphase-promoting complex subunit 2Nprotein822Homo sapiensQ9UJX6

5 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>6TM5_1 Anaphase-promoting complex subunit 1 (chains A)
MSNFYEERTTMIAARDLQEFVPFGRDHCKHHPNALNLQLRQLQPASELWSSDGAAGLVGS
LQEVTIHEKQKESWQLRKGVSEIGEDVDYDEELYVAGNMVIWSKGSKSQALAVYKAFTVD
SPVQQALWCDFIISQDKSEKAYSSNEVEKCICILQSSCINMHSIEGKDYIASLPFQVANV
WPTKYGLLFERSASSHEVPPGSPREPLPTMFSMLHPLDEITPLVCKSGSLFGSSRVQYVV
DHAMKIVFLNTDPSIVMTYDAVQNVHSVWTLRRVKSEEENVVLKFSEQGGTPQNVATSSS
LTAHLRSLSKGDSPVTSPFQNYSSIHSQSRSTSSPSLHSRSPSISNMAALSRAHSFALGV
HSFSGVQRFNISSHNQSPKRHSISHSPNSNSNGSFLAPETEPIVPELCIDHLWTETITNI
REKNSQASKVFITSDLCGQKFLCFLVESQLQLRCVKFQESNDKTQLIFGSVTNIPAKDAA
PVEKIDTMLVLEGSGNLVLYTGVVRVGKVFIPGLPAPSLTMSNTMPRPSTPLDGVSTPKP
LSKLLGSLDEVVLLSPVPELRDSSKLHDSLYNEDCTFQQLGTYIHSIRDPVHNRVTLELS
NGSMVRITIPEIATSELVQTCLQAIKFILPKEIAVQMLVKWYNVHSAPGGPSYHSEWNLF
VTCLMNMMGYNTDRLAWTRNFDFEGSLSPVIAPKKARPSETGSDDDWEYLLNSDYHQNVE
SHLLNRSLCLSPSEASQMKDEDFSQNLSLDSSTLLFTHIPAIFFVLHLVYEELKLNTLMG
EGICSLVELLVQLARDLKLGPYVDHYYRDYPTLVRTTGQVCTIDPGQTGFMHHPSFFTSE
PPSIYQWVSSCLKGEGMPPYPYLPGICERSRLVVLSIALYILGDESLVSDESSQYLTRIT
IAPQKLQVEQEENRFSFRHSTSVSSLAERLVVWMTNVGFTLRDLETLPFGIALPIRDAIY
HCREQPASDWPEAVCLLIGRQDLSKQACEGNLPKGKSVLSSDVPSGTETEEEDDGMNDMN
HEVMSLIWSEDLRVQDVRRLLQSAHPVRVNVVQYPELSDHEFIEEKENRLLQLCQRTMAL
PVGRGMFTLFSYHPVPTEPLPIPKLNLTGRAPPRNTTVDLNSGNIDVPPNMTSWASFHNG
VAAGLKIAPASQIDSAWIVYNKPKHAELANEYAGFLMALGLNGHLTKLATLNIHDYLTKG
HEMTSIGLLLGVSAAKLGTMDMSITRLLSIHIPALLPPTSTELDVPHNVQVAAVVGIGLV
YQGTAHRHTAEVLLAEIGRPPGPEMEYCTDRESYSLAAGLALGMVCLGHGSNLIGMSDLN
VPEQLYQYMVGGHRRFQTGMHREKHKSPSYQIKEGDTINVDVTCPGATLALAMIYLKTNN
RSIADWLRAPDTMYLLDFVKPEFLLLRTLARCLILWDDILPNSKWVDSNVPQIIRENSIS
LSEIELPCSEDLNLETLSQAHVYIIAGACLSLGFRFAGSENLSAFNCLHKFAKDFMTYLS
APNASVTGPHNLETCLSVVLLSLAMVMAGSGNLKVLQLCRFLHMKTGGEMNYGFHLAHHM
ALGLLFLGGGRYSLSTSNSSIAALLCALYPHFPAHSTDNRYHLQALRHLYVLAAEPRLLV
PVDVDTNTPCYALLEVTYKGTQWYEQTKEELMAPTLLPELHLLKQIKVKGPRYWELLIDL
SKGTQHLKSILSKDGVLYVKLRAGQLSYKEDPMGWQSLLAQTVANRNSEARAFKPETISA
FTSDPALLSFAEYFCKPTVNMGQKQEILDLFSSVLYECVTQETPEMLPAYIAMDQAIRRL
GRREMSETSELWQIKLVLEFFSSRSHQERLQNHPKRGLFMNSEFLPVVKCTIDNTLDQWL
QVGGDMCVHAYLSGQPLEESQLSMLACFLVYHSVPAPQHLPPIGLEGSTSFAELLFKFKQ
LKMPVRALLRLAPLLLGNPQPMVM
Sequence of entity 2 (B), FASTA
>6TM5_2 Anaphase-promoting complex subunit 11 (chains B)
MKVKIKCWNGVATWLWVANDENCGICRMAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCI
LKWLHAQQVQQHCPMCRQEWKFKE
Sequence of entity 3 (C, P), FASTA
>6TM5_3 Cell division cycle protein 23 homolog (chains C, P)
MAASTSMVPVAVTAAVAPVLSINSDFSDLREIKKQLLLIAGLTRERGLLHSSKWSAELAF
SLPALPLAELQPPPPITEEDAQDMDAYTLAKAYFDVKEYDRAAHFLHGCNSKKAYFLYMY
SRYLSGEKKKDDETVDSLGPLEKGQVKNEALRELRVELSKKHQARELDGFGLYLYGVVLR
KLDLVKEAIDVFVEATHVLPLHWGAWLELCNLITDKEMLKFLSLPDTWMKEFFLAHIYTE
LQLIEEALQKYQNLIDVGFSKSSYIVSQIAVAYHNIRDIDKALSIFNELRKQDPYRIENM
DTFSNLLYVRSMKSELSYLAHNLCEIDKYRVETCCVIGNYYSLRSQHEKAALYFQRALKL
NPRYLGAWTLMGHEYMEMKNTSAAIQAYRHAIEVNKRDYRAWYGLGQTYEILKMPFYCLY
YYRRAHQLRPNDSRMLVALGECYEKLNQLVEAKKCYWRAYAVGDVEKMALVKLAKLHEQL
TESEQAAQCYIKYIQDIYSCGEIVEHLEESTAFRYLAQYYFKCKLWDEASTCAQKCCAFN
DTREEGKALLRQILQLRNQGETPTTEVPAPFFLPASLSANNTPTRRVSPLNLSSVTP
Sequence of entity 4 (D), FASTA
>6TM5_4 Anaphase-promoting complex subunit 15 (chains D)
MSTLFPSLFPRVTETLWFNLDRPCVEETELQQQEQQHQAWLQSIAEKDNNLVPIGKPASE
HYDDEEEEDDEDDEDSEEDSEDDEDMQDMDEMNDYNESPDDGEVNEVDMEGNEQDQDQWM
I
Sequence of entity 5 (E), FASTA
>6TM5_5 Anaphase-promoting complex subunit 16 (chains E)
MAASSSSSSAGGVSGSSVTGSGFSVSDLAPPRKALFTYPKGAGEMLEDGSERFLCESVFS
YQVASTLKQVKHDQQVARMEKLAGLVEELEADEWRFKPIEQLLGFTPSSG
Sequence of entity 6 (F, H), FASTA
>6TM5_6 Cell division cycle protein 27 homolog (chains F, H)
MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRSGKAYKAYRL
LKGHSCTTPQCKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSL
LGHVYCKTDRLAKGSECYQKSLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCL
PNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLNLESSNSKYSLNTDSSVSYIDSAVI
SPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILPLETPSPGDGSYLQN
YTNTPPVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQTQSSGPQTSTTP
QVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQ
PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYN
CKEAINILSHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYS
TTLWHLQKDVALSVLSKDLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNY
AYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAWYGLGMIYYKQEKFSLAEMHFQK
ALDINPQSSVLLCHIGVVQHALKKSEKALDTLNKAIVIDPKNPLCKFHRASVLFANEKYK
SALQELEELKQIVPKESLVYFLIGKVYKKLGQTHLALMNFSWAMDLDPKGANNQIKEAID
KRYLPDDEEPITQEEQIMGTDESQESSMTDADDTQLHAAESDEF
Sequence of entity 7 (G, W), FASTA
>6TM5_7 Anaphase-promoting complex subunit CDC26 (chains G, W)
MLRRKPTRLELKLDDIEEFENIRKDLETRKKQKEDVEVVGGSDGEGAIGLSSDPKSREQM
INDRIGYKPQPKPNNRSSQFGSLEF
Sequence of entity 8 (I), FASTA
>6TM5_8 Anaphase-promoting complex subunit 4 (chains I)
MLRFPTCFPSFRVVGEKQLPQEIIFLVWSPKRDLIALANTAGEVLLHRLASFHRVWSFPP
NENTGKEVTCLAWRPDGKLLAFALADTKKIVLCDVEKPESLHSFSVEAPVSCMHWMEVTV
ESSVLTSFYNAEDESNLLLPKLPTLPKNYSNTSKIFSEENSDEIIKLLGDVRLNILVLGG
SSGFIELYAYGMFKIARVTGIAGTCLALCLSSDLKSLSVVTEVSTNGASEVSYFQLETNL
LYSFLPEVTRMARKFTHISALLQYINLSLTCMCEAWEEILMQMDSRLTKFVQEKNTTTSV
QDEFMHLLLWGKASAELQTLLMNQLTVKGLKKLGQSIESSYSSIQKLVISHLQSGSESLL
YHLSELKGMASWKQKYEPLGLDAAGIEEAITAVGSFILKANELLQVIDSSMKNFKAFFRW
LYVAMLRMTEDHVLPELNKMTQKDITFVAEFLTEHFNEAPDLYNRKGKYFNVERVGQYLK
DEDDDLVSPPNTEGNQWYDFLQNSSHLKESPLLFPYYPRKSLHFVKRRMENIIDQCLQKP
ADVIGKSMNQAICIPLYRDTRSEDSTRRLFKFPFLWNNKTSNLHYLLFTILEDSLYKMCI
LRRHTDISQSVSNGLIAIKFGSFTYATTEKVRRSIYSCLDAQFYDDETVTVVLKDTVGRE
GRDRLLVQLPLSLVYNSEDSAEYQFTGTYSTRLDEQCSAIPTRTMHFEKHWRLLESMKAQ
YVAGNGFRKVSCVLSSNLRHVRVFEMDIDDEWELDESSDEEEEASNKPVKIKEEVLSESE
AENQQAGAAALAPEIVIKVEKLDPELDS
Sequence of entity 9 (J, K), FASTA
>6TM5_9 Cell division cycle protein 16 homolog (chains J, K)
MNLERLRKRVRQYLDQQQYQSALFWADKVASLSREEPQDIYWLAQCLYLTAQYHRAAHAL
RSRKLDKLYEACRYLAARCHYAAKEHQQALDVLDMEEPINKRLFEKYLKDESGFKDPSSD
WEMSQSSIKSSICLLRGKIYDALDNRTLATYSYKEALKLDVYCFEAFDLLTSHHMLTAQE
EKELLESLPLSKLCNEEQELLRFLFENKLKKYNKPSETVIPESVDGLQENLDVVVSLAER
HYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPV
SWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTA
AQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKT
AEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNAS
TYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCIEMYIGDSEAYIGADIKD
KLKCYDFDVHTMKTLKNIISPPWDFREFEVEKQTAEETGLTPLETSRKTPDSRPSLEETF
EIEMNESDMMLETSMSDHST
Sequence of entity 10 (L), FASTA
>6TM5_10 Anaphase-promoting complex subunit 10 (chains L)
MTTPNKTPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQ
PHLVNIQFRRKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWI
HVPLTDNHKKPTRTFMIQIAVLANHQNGRDTHMRQIKIYTPVEESSIGKFPRCTTIDFMM
YRSIR
Sequence of entity 11 (M), FASTA
>6TM5_11 Anaphase-promoting complex subunit 13 (chains M)
MDSEVQRDGRILDLIDDAWREDKLPYEDVAIPLNELPEPEQDNGGTTESVKEQEMKWTDL
ALQYLHENVPPIGN
Sequence of entity 12 (N), FASTA
>6TM5_12 Anaphase-promoting complex subunit 2 (chains N)
MAAAVVVAEGDSDSRPGQELLVAWNTVSTGLVPPAALGLVSSRTSGAVPPKEEELRAAVE
VLRGHGLHSVLEEWFVEVLQNDLQANISPEFWNAISQCENSADEPQCLLLLLDAFGLLES
RLDPYLRSLELLEKWTRLGLLMGTGAQGLREEVHTMLRGVLFFSTPRTFQEMIQRLYGCF
LRVYMQSKRKGEGGTDPELEGELDSRYARRRYYRLLQSPLCAGCSSDKQQCWCRQALEQF
HQLSQVLHRLSLLERVSAEAVTTTLHQVTRERMEDRCRGEYERSFLREFHKWIERVVGWL
GKVFLQDGPARPASPEAGNTLRRWRCHVQRFFYRIYASLRIEELFSIVRDFPDSRPAIED
LKYCLERTDQRQQLLVSLKAALETRLLHPGVNTCDIITLYISAIKALRVLDPSMVILEVA
CEPIRRYLRTREDTVRQIVAGLTGDSDGTGDLAVELSKTDPASLETGQDSEDDSGEPEDW
VPDPVDADPGKSSSKRRSSDIISLLVSIYGSKDLFINEYRSLLADRLLHQFSFSPEREIR
NVELLKLRFGEAPMHFCEVMLKDMADSRRINANIREEDEKRPAEEQPPFGVYAVILSSEF
WPPFKDEKLEVPEDIRAALEAYCKKYEQLKAMRTLSWKHTLGLVTMDVELADRTLSVAVT
PVQAVILLYFQDQASWTLEELSKAVKMPVALLRRRMSVWLQQGVLREEPPGTFSVIEEER
PQDRDNMVLIDSDDESDSGMASQADQKEEELLLFWTYIQAMLTNLESLSLDRIYNMLRMF
VVTGPALAEIDLQELQGYLQKKVRDQQLVYSAGVYRLPKNCS

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn3

Primary citation

A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase. Alfieri, C., Tischer, T., Barford, D. EMBO Rep (2020) 21:e49831-e49831. DOI 10.15252/embr.201949831 · PubMed

Other PDB entries of the same protein (UniProt Q9H1A4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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