3JC6: DNA replication licensing factor MCM2

Structure of the eukaryotic replicative CMG helicase and pumpjack motion. Determined by electron microscopy at 3.7 Å resolution. Released 10 Feb 2016.

Method
Electron microscopy
Resolution
3.7 Å
Organism
Saccharomyces cerevisiae
Chains
11
Atoms
23,732
Mol. weight
788.77 kDa
Ligands
ZN
Released
10 Feb 2016

Explore 3JC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JC6 contains 119 α-helices and 132 β-strands across 11 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 2: 11 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix203-21513
α-helix226-23611
α-helix246-2527
α-helix254-2607
α-helix264-28219
α-helix311-3133
β-strand31411
β-strand31711
β-strand320-32561
α-helix326-3294
β-strand331-33331
β-strand383-39191
α-helix394-3963
α-helix397-3982
β-strand405-41171
α-helix412-4143
β-strand423-42641
α-helix4281
β-strand429-43131
β-strand44612
β-strand450-45231
β-strand456-45831
Chain 3: 12 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix19-3113
α-helix39-5416
α-helix100-1023
α-helix103-1064
α-helix108-1169
α-helix118-1203
α-helix122-13413
β-strand179-18023
β-strand184-18634
α-helix190-1923
β-strand19315
β-strand19616
β-strand198-20367
β-strand210-21347
β-strand241-24337
β-strand25016
β-strand25315
β-strand255-25954
α-helix260-2612
α-helix262-2643
α-helix270-2712
β-strand274-27744
α-helix280-2823
β-strand291-29334
β-strand296-29723
β-strand298-30034
β-strand319-32134
β-strand327-32824
Chain 4: 9 helices, 21 β-strands
ElementResiduesLengthSheet
α-helix190-1956
α-helix227-23610
β-strand24118
α-helix255-2639
α-helix265-28420
α-helix295-2984
β-strand30318
β-strand32519
β-strand328110
β-strand332-335411
α-helix336-3383
β-strand339-342412
β-strand344-345213
β-strand348114
β-strand358-359213
β-strand365-366215
α-helix380-3823
β-strand383114
β-strand391-394412
β-strand397-400411
α-helix411-4133
β-strand414-417411
α-helix421-4233
β-strand435-436210
β-strand43819
β-strand439-442411
β-strand445116
β-strand453116
β-strand458-461411
β-strand465-466210
Chain 5: 13 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix22-3615
α-helix45-5511
β-strand60-63417
α-helix65-717
α-helix73-797
α-helix83-10119
α-helix133-1353
β-strand136-139417
α-helix148-1503
β-strand162-169818
α-helix170-1723
β-strand173119
β-strand176-183820
β-strand190-193420
α-helix206-2083
β-strand241-2501020
β-strand253119
β-strand256-260518
α-helix2611
α-helix270-2723
β-strand273-277518
β-strand279119
α-helix280-2823
β-strand291-294418
β-strand298-301418
α-helix3241
β-strand325-329518
β-strand334-335218
Chain 6: 6 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix107-12014
α-helix136-14611
β-strand150-154521
α-helix155-1628
α-helix165-1695
α-helix174-1774
α-helix178-19215
β-strand264-268521
β-strand273-274222
β-strand289-290222
β-strand292-295423
β-strand30312
β-strand35412
β-strand357-362623
β-strand377-381523
β-strand391123
β-strand394-395223
β-strand396-397224
β-strand404-405225
β-strand419-420215
β-strand450-451225
β-strand454-456323
β-strand459-460224
Chain 7: 10 helices, 18 β-strands
ElementResiduesLengthSheet
β-strand717
α-helix14-2411
α-helix62-7110
β-strand77-81526
α-helix82-9110
α-helix103-1097
α-helix112-1154
α-helix120-1245
α-helix140-15718
β-strand201-205526
α-helix217-2193
β-strand225127
β-strand239-246827
α-helix249-2513
β-strand252-253227
β-strand256128
β-strand259-262429
β-strand269-270229
β-strand278116
β-strand298-300329
β-strand306128
β-strand309-316827
β-strand331-336627
α-helix337-3393
β-strand348-353627
β-strand355127
β-strand376-377227
β-strand380-383427
Chain A: 6 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix4-2118
α-helix35-5723
α-helix58-625
α-helix68-10336
α-helix125-14420
β-strand162-166530
β-strand188-192530
α-helix193-2008
Chain B: 11 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix11-122
α-helix13-208
β-strand24-29639
α-helix62-643
β-strand69-72439
α-helix73-819
β-strand85-87339
α-helix88-903
α-helix95-10612
α-helix119-12810
α-helix130-1323
α-helix141-15919
α-helix160-1623
β-strand164140
β-strand167140
β-strand169138
α-helix175-19824

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA replication licensing factor MCM22protein868Saccharomyces cerevisiaeP29469 (AlphaFold model)
DNA replication licensing factor MCM33protein971Saccharomyces cerevisiaeP24279 (AlphaFold model)
DNA replication licensing factor MCM44protein933Saccharomyces cerevisiaeP30665 (AlphaFold model)
Minichromosome maintenance protein 55protein775Saccharomyces cerevisiaeP29496 (AlphaFold model)
DNA replication licensing factor MCM66protein1017Saccharomyces cerevisiaeP53091
DNA replication licensing factor MCM77protein845Saccharomyces cerevisiaeP38132
Cell division control protein 45Eprotein672Saccharomyces cerevisiaeQ08032
DNA replication complex GINS protein SLD5Dprotein294Saccharomyces cerevisiaeQ03406
DNA replication complex GINS protein PSF2Bprotein213Saccharomyces cerevisiaeP40359
DNA replication complex GINS protein PSF1Aprotein208Saccharomyces cerevisiaeQ12488
DNA replication complex GINS protein PSF3Cprotein194Saccharomyces cerevisiaeQ12146
Sequence of entity 1 (2), FASTA
>3JC6_1 DNA replication licensing factor MCM2 (chains 2)
MSDNRRRRREEDDSDSENELPPSSPQQHFRGGMNPVSSPIGSPDMINPEGDDNEVDDVPD
IDEVEEQMNEVDLMDDNMYEDYAADHNRDRYDPDQVDDREQQELSLSERRRIDAQLNERD
RLLRNVAYIDDEDEEQEGAAQLDEMGLPVQRRRRRRQYEDLENSDDDLLSDMDIDPLREE
LTLESLSNVKANSYSEWITQPNVSRTIARELKSFLLEYTDETGRSVYGARIRTLGEMNSE
SLEVNYRHLAESKAILALFLAKCPEEMLKIFDLVAMEATELHYPDYARIHSEIHVRISDF
PTIYSLRELRESNLSSLVRVTGVVTRRTGVFPQLKYVKFNCLKCGSILGPFFQDSNEEIR
ISFCTNCKSKGPFRVNGEKTVYRNYQRVTLQEAPGTVPPGRLPRHREVILLADLVDVSKP
GEEVEVTGIYKNNYDGNLNAKNGFPVFATIIEANSIKRREGNTANEGEEGLDVFSWTEEE
EREFRKISRDRGIIDKIISSMAPSIYGHRDIKTAVACSLFGGVPKNVNGKHSIRGDINVL
LLGDPGTAKSQILKYVEKTAHRAVFATGQGASAVGLTASVRKDPITKEWTLEGGALVLAD
KGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTTLQARCSIIAAANPNGGRYNST
LPLAQNVSLTEPILSRFDILCVVRDLVDEEADERLATFVVDSHVRSHPENDEDREGEELK
NNGESAIEQGEDEINEQLNARQRRLQRQRKKEEEISPIPQELLMKYIHYARTKIYPKLHQ
MDMDKVSRVYADLRRESISTGSFPITVRHLESILRIAESFAKMRLSEFVSSYDLDRAIKV
VVDSFVDAQKVSVRRQLRRSFAIYTLGH
Sequence of entity 2 (3), FASTA
>3JC6_2 DNA replication licensing factor MCM3 (chains 3)
MEGSTGFDGDATTFFAPDAVFGDRVRRFQEFLDTFTSYRDSVRSIQVYNSNNAANYNDDQ
DDADERDLLGDDDGDDLEKEKKAASSTSLNILPHRIIISLDDLREFDRSFWSGILVEPAY
FIPPAEKALTDLADSMDDVPHPNASAVSSRHPWKLSFKGSFGAHALSPRTLTAQHLNKLV
SVEGIVTKTSLVRPKLIRSVHYAAKTGRFHYRDYTDATTTLTTRIPTPAIYPTEDTEGNK
LTTEYGYSTFIDHQRITVQEMPEMAPAGQLPRSIDVILDDDLVDKTKPGDRVNVVGVFKS
LGAGGMNQSNSNTLIGFKTLILGNTVYPLHARSTGVAARQMLTDFDIRNINKLSKKKDIF
DILSQSLAPSIYGHDHIKKAILLMLMGGVEKNLENGSHLRGDINILMVGDPSTAKSQLLR
FVLNTASLAIATTGRGSSGVGLTAAVTTDRETGERRLEAGAMVLADRGVVCIDEFDKMTD
VDRVAIHEVMEQQTVTIAKAGIHTTLNARCSVIAAANPVFGQYDVNRDPHQNIALPDSLL
SRFDLLFVVTDDINEIRDRSISEHVLRTHRYLPPGYLEGEPVRERLNLSLAVGEDADINP
EEHSNSGAGVENEGEDDEDHVFEKFNPLLQAGAKLAKNKGNYNGTEIPKLVTIPFLRKYV
QYAKERVIPQLTQEAINVIVKNYTDLRNDDNTKKSPITARTLETLIRLATAHAKVRLSKT
VNKVDAKVAANLLRFALLGEDIGNDIDEEESEYEEALSKRSPQKSPKKRQRVRQPASNSG
SPIKSTPRRSTASSVNATPSSARRILRFQDDEQNAGEDDNDIMSPLPADEEAELQRRLQL
GLRVSPRRREHLHAPEEGSSGPLTEVGTPRLPNVSSAGQDDEQQQSVISFDNVEPGTIST
GRLSLISGIIARLMQTEIFEEESYPVASLFERINEELPEEEKFSAQEYLAGLKIMSDRNN
LMVADDKVWRV
Sequence of entity 3 (4), FASTA
>3JC6_3 DNA replication licensing factor MCM4 (chains 4)
MSQQSSSPTKEDNNSSSPVVPNPDSVPPQLSSPALFYSSSSSQGDIYGRNNSQNLSQGEG
NIRAAIGSSPLNFPSSSQRQNSDVFQSQGRQGRIRSSASASGRSRYHSDLRSDRALPTSS
SSLGRNGQNRVHMRRNDIHTSDLSSPRRIVDFDTRSGVNTLDTSSSSAPPSEASEPLRII
WGTNVSIQECTTNFRNFLMSFKYKFRKILDEREEFINNTTDEELYYIKQLNEMRELGTSN
LNLDARNLLAYKQTEDLYHQLLNYPQEVISIMDQTIKDCMVSLIVDNNLDYDLDEIETKF
YKVRPYNVGSCKGMRELNPNDIDKLINLKGLVLRSTPVIPDMKVAFFKCNVCDHTMAVEI
DRGVIQEPARCERIDCNEPNSMSLIHNRCSFADKQVIKLQETPDFVPDGQTPHSISLCVY
DELVDSCRAGDRIEVTGTFRSIPIRANSRQRVLKSLYKTYVDVVHVKKVSDKRLDVDTST
IEQELMQNKVDHNEVEEVRQITDQDLAKIREVAAREDLYSLLARSIAPSIYELEDVKKGI
LLQLFGGTNKTFTKGGRYRGDINILLCGDPSTSKSQILQYVHKITPRGVYTSGKGSSAVG
LTAYITRDVDTKQLVLESGALVLSDGGVCCIDEFDKMSDSTRSVLHEVMEQQTISIAKAG
IITTLNARSSILASANPIGSRYNPNLPVTENIDLPPPLLSRFDLVYLVLDKVDEKNDREL
AKHLTNLYLEDKPEHISQDDVLPVEFLTMYISYAKEHIHPIITEAAKTELVRAYVGMRKM
GDDSRSDEKRITATTRQLESMIRLAEAHAKMKLKNVVELEDVQEAVRLIRSAIKDYATDP
KTGKIDMNLVQTGKSVIQRKLQEDLSREIMNVLKDQASDSMSFNELIKQINEHSQDRVES
SDIQEALSRLQQEDKVIVLGEGVRRSVRLNNRV
Sequence of entity 4 (5), FASTA
>3JC6_4 Minichromosome maintenance protein 5 (chains 5)
MSFDRPEIYSAPVLQGESPNDDDNTEIIKSFKNFILEFRLDSQFIYRDQLRNNILVKNYS
LTVNMEHLIGYNEDIYKKLSDEPSDIIPLFETAITQVAKRISILSRAQSANNNDKDPENT
SMDTDSLLLNSLPTFQLILNSNANQIPLRDLDSEHVSKIVRLSGIIISTSVLSSRATYLS
IMCRNCRHTTSITINNFNSITGNTVSLPRSCLSTIESESSMANESNIGDESTKKNCGPDP
YIIIHESSKFIDQQFLKLQEIPELVPVGEMPRNLTMTCDRYLTNKVIPGTRVTIVGIYSI
YNSKNGAGSGRSGGGNGGSGVAIRTPYIKILGIQSDVETSSIWNSVTMFTEEEEEEFLQL
SRNPKLYEILTNSIAPSIFGNEDIKKAIVCLLMGGSKKILPDGMRLRGDINVLLLGDPGT
AKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVQRDPMTREFYLEGGAMVLADGGVVCID
EFDKMRDEDRVAIHEAMEQQTISIAKAGITTVLNSRTSVLAAANPIYGRYDDLKSPGDNI
DFQTTILSRFDMIFIVKDDHNEERDISIANHVINIHTGNANAMQNQQEENGSEISIEKMK
RYITYCRLKCAPRLSPQAAEKLSSNFVTIRKQLLINELESTERSSIPITIRQLEAIIRIT
ESLAKLELSPIAQERHVDEAIRLFQASTMDAASQDPIGGLNQASGTSLSEIRRFEQELKR
RLPIGWSTSYQTLRREFVDTHRFSQLALDKALYALEKHETIQLRHQGQNIYRSGV
Sequence of entity 5 (6), FASTA
>3JC6_5 DNA replication licensing factor MCM6 (chains 6)
MSSPFPADTPSSNRPSNSSPPPSSIGAGFGSSSGLDSQIGSRLHFPSSSQPHVSNSQTGP
FVNDSTQFSSQRLQTDGSATNDMEGNEPARSFKSRALNHVKKVDDVTGEKVREAFEQFLE
DFSVQSTDTGEVEKVYRAQIEFMKIYDLNTIYIDYQHLSMRENGALAMAISEQYYRFLPF
LQKGLRRVVRKYAPELLNTSDSLKRSEGDEGQADEDEQQDDDMNGSSLPRDSGSSAAPGN
GTSAMATRSITTSTSPEQTERVFQISFFNLPTVHRIRDIRSEKIGSLLSISGTVTRTSEV
RPELYKASFTCDMCRAIVDNVEQSFKYTEPTFCPNPSCENRAFWTLNVTRSRFLDWQKVR
IQENANEIPTGSMPRTLDVILRGDSVERAKPGDRCKFTGVEIVVPDVTQLGLPGVKPSST
LDTRGISKTTEGLNSGVTGLRSLGVRDLTYKISFLACHVISIGSNIGASSPDANSNNRET
ELQMAANLQANNVYQDNERDQEVFLNSLSSDEINELKEMVKDEHIYDKLVRSIAPAVFGH
EAVKKGILLQMLGGVHKSTVEGIKLRGDINICVVGDPSTSKSQFLKYVVGFAPRSVYTSG
KASSAAGLTAAVVRDEEGGDYTIEAGALMLADNGICCIDEFDKMDISDQVAIHEAMEQQT
ISIAKAGIHATLNARTSILAAANPVGGRYNRKLSLRGNLNMTAPIMSRFDLFFVILDDCN
EKIDTELASHIVDLHMKRDEAIEPPFSAEQLRRYIKYARTFKPILTKEARSYLVEKYKEL
RKDDAQGFSRSSYRITVRQLESMIRLSEAIARANCVDEITPSFIAEAYDLLRQSIIRVDV
DDVEMDEEFDNIESQSHAASGNNDDNDDGTGSGVITSEPPADIEEGQSEATARPGTSEKK
KTTVTYDKYVSMMNMIVRKIAEVDREGAEELTAVDIVDWYLLQKENDLGSLAEYWEERRL
AFKVIKRLVKDRILMEIHGTRHNLRDLENEENENNKTVYVIHPNCEVLDQLEPQDSS
Sequence of entity 6 (7), FASTA
>3JC6_6 DNA replication licensing factor MCM7 (chains 7)
MSAALPSIQLPVDYNNLFNEITDFLVTFKQDTLSSDATRNENEDENLDAENIEQHLLEKG
PKYMAMLQKVANRELNSVIIDLDDILQYQNEKFLQGTQADDLVSAIQQNANHFTELFCRA
IDNNMPLPTKEIDYKDDVLDVILNQRRLRNERMLSDRTNEIRSENLMDTTMDPPSSMNDA
LREVVEDETELFPPNLTRRYFLYFKPLSQNCARRYRKKAISSKPLSVRQIKGDFLGQLIT
VRGIITRVSDVKPAVEVIAYTCDQCGYEVFQEVNSRTFTPLSECTSEECSQNQTKGQLFM
STRASKFSAFQECKIQELSQQVPVGHIPRSLNIHVNGTLVRSLSPGDIVDVTGIFLPAPY
TGFKALKAGLLTETYLEAQFVRQHKKKFASFSLTSDVEERVMELITSGDVYNRLAKSIAP
EIYGNLDVKKALLLLLVGGVDKRVGDGMKIRGDINVCLMGDPGVAKSQLLKAICKISPRG
VYTTGKGSSGVGLTAAVMKDPVTDEMILEGGALVLADNGICCIDEFDKMDESDRTAIHEV
MEQQTISISKAGINTTLNARTSILAAANPLYGRYNPRLSPLDNINLPAALLSRFDILFLM
LDIPSRDDDEKLAEHVTYVHMHNKQPDLDFTPVEPSKMREYIAYAKTKRPVMSEAVNDYV
VQAYIRLRQDSKREMDSKFSFGQATPRTLLGIIRLSQALAKLRLADMVDIDDVEEALRLV
RVSKESLYQETNKSKEDESPTTKIFTIIKKMLQETGKNTLSYENIVKTVRLRGFTMLQLS
NCIQEYSYLNVWHLINEGNTLKFVDDGTMDTDQEDSLVSTPKLAPQTTASANVSAQDSDI
DLQDA
Sequence of entity 7 (E), FASTA
>3JC6_7 Cell division control protein 45 (chains E)
MYYGISQFSEAYNKILRNSSSHSSCQLVIFVSCLNIDALCATKMLSLLFKKQLVQSQIVP
IFGYSELRRHYSQLDDNINSLLLVGFGGVIDLEAFLEIDPQEYVIDTDEKSGEQSFRRDI
YVLDAHRPWNLDNIFGSQIIQCFDDGTVDDTLGEQKEAYYKLLELDEESGDDELSGDEND
NNGGDDEATDADEVTDEDEEDEDETISNKRGNSSIGPNDLSKRKQRKKQIHEYEGVLEEY
YSQGTTVVNSISAQIYSLLSAIGETNLSNLWLNILGTTSLDIAYAQVYNRLYPLLQDEVK
RLTPSSRNSVKTPDTLTLNIQPDYYLFLLRHSSLYDSFYYSNYVNAKLSLWNENGKKRLH
KMFARMGIPLSTAQETWLYMDHSIKRELGIIFDKNLDRYGLQDIIRDGFVRTLGYRGSIS
ASEFVEALTALLEVGNSTDKDSVKINNDNNDDTDGEEEEDNSAQKLTNLRKRWVSNFWLS
WDALDDRKVELLNRGIQLAQDLQRAIFNTGVAILEKKLIKHLRIYRLCVLQDGPDLDLYR
NPLTLLRLGNWLIECCAESEDKQLLPMVLASIDENTDTYLVAGLTPRYPRGLDTIHTKKP
ILNNFSMAFQQITAETDAKVRIDNFESSIIEIRREDLSPFLEKLTLSGLLDYKDHDGDYK
DHDIDYKDDDDK
Sequence of entity 8 (D), FASTA
>3JC6_8 DNA replication complex GINS protein SLD5 (chains D)
MDINIDDILAELDKETTAVDSTKITQGSSSTTHRDANTIVGSSLDLNDKTQIYVSPQQDF
SDLMKSWKNERCSPELLPYPHQLMKRLLNRISMQSQLIENISMGFLDMQNASNANPPMPN
ESKLPLLCMETELERLKFVIRSYIRCRLSKIDKFSLYLRQLNEDENSLISLTDLLSKDEI
KYHDTHSLIWLKLVNDSILKYMPEELQAINDTEGSVNMIDEPDWNKFVFIHVNGPPDGKW
NEDPLLQENEFGKPCYTVTIPDLKEEVELTIGSIYVMRYEVIRDLLRDDKVALI
Sequence of entity 9 (B), FASTA
>3JC6_9 DNA replication complex GINS protein PSF2 (chains B)
MSLPAHLQQTFSPEEIQFIVENEPIKIFPRITTRQKIRGDDRGTGNHTRWQLITTDDKAL
NNMVAMRSTEVVLWIALLLKQQSKCSIVAPQWLTTKELDRKIQYEKTHPDRFSELPWNWL
VLARILFNKAKDDFHDPIHELRGKIQDLREIRQIKVLKGLKYLNESHLQLDNLSLLEINE
LRPFITEIMDKLREIHTASLTAGTENDEEEFNI
Sequence of entity 10 (A), FASTA
>3JC6_10 DNA replication complex GINS protein PSF1 (chains A)
MYGDLGNKLVLEAKRTKQLYARSNQDVNLPMYHEDIIRNILKEVSNLRKNTEYLKEQQQL
GMLDDKVAKCQYFVTLLCMERNKRCLLAYQRLRTDILDSMAWNNNGLDLMSSITFSQQDT
NNLSHQEQEYLKEYCDLITDLKSGDLVDIDLSGSLVPPSDVFIDVRVLKDAGEIQTEYGV
FNLIKDSQFFVRQSDVERLIQQGYLQKI
Sequence of entity 11 (C), FASTA
>3JC6_11 DNA replication complex GINS protein PSF3 (chains C)
MGYYDIDDVLADGTEFPCKFQYDIPGLGYLENNPGRPITKNTKLSLPLWLARILAIVGGD
EALVDEEPVPFVELLPPDMFSTKVMNAIKTDPVALDLHSINSHFFSLAIKWIMLFSEKEL
ANVVSELLLQRAQELNHHASSLSIDLNADSTGKNSANTNIATSTFLLKLEEMEKEIYKKS
HESYKDTKRWMFKK

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1

Primary citation

Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation. Yuan, Z., Bai, L., Sun, J. et al. Nat Struct Mol Biol (2016) 23:217-224. DOI 10.1038/nsmb.3170 · PubMed

Other PDB entries of the same protein (UniProt P29469 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 3JC6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.