Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (composite map)

2026-09-23 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update PDBe PDBe 2025-12-03 2026-08-26 2026-08-26 2026-09-23 Wellcome Trust 107903/Z/15/Z United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/T005378/1 United Kingdom Cancer Research UK DRCNPG-May21/100006 United Kingdom Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (composite map) Saleh A Noguchi Y Schneider S Aramayo R Speck C Helicase, Activation, Phosphorylation, REPLICATION Noguchi Y Saleh A Schneider S Ivanova ME Chen ZA Ranjha L Aramayo R Tognetti S Faull SV Rappsilber J Speck C Structural insights into Sld3-Sld7-dependent Cdc45 loading during replication initiation. Nat Commun UK 17 2026 42733061 doi:10.1038/s41467-026-76309-6 2041-1723 EMD-55985 consensus EM volume

MSC consensus map

EMD-55986 focused EM volume

C2 DH core focused map

EMD-55987 focused EM volume

Sld3 MRD1/2:Mcm4/6 focused map

EMD-55988 focused EM volume

Sld7:Mcm6 focused map

EMD-55989 focused EM volume

Sld3 STD/Cdc45:Mcm2/5 focused map

9th8 FULLOVERLAP EMDB EMD-55918 associated EM volume

Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

EMDB EMD-55985 consensus EM volume

MSC consensus map

EMDB EMD-55986 focused EM volume

C2 DH core focused map

EMDB EMD-55987 focused EM volume

Sld3 MRD1/2:Mcm4/6 focused map

EMDB EMD-55988 focused EM volume

Sld7:Mcm6 focused map

EMDB EMD-55989 focused EM volume

Sld3 STD/Cdc45:Mcm2/5 focused map

MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA 0 1 2 3 4 5 6 7 8 9 10 11 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 1.65 dsDNA (60-MER) Saccharomyces cerevisiae 0.018491848 1 (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) DNA dsDNA (60-MER) Saccharomyces cerevisiae 0.018491848 1 (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) DNA DNA replication licensing factor MCM2 Saccharomyces cerevisiae 0.098911539 2 Saccharomyces cerevisiae LEVO MSDNRRRRREEDDSDSENELPPSSPQQHFRGGMNPVSSPIGSPDMINPEGDDNEVDDVPDIDEVEEQMNEVDLMDDNMYE DYAADHNRDRYDPDQVDDREQQELSLSERRRIDAQLNERDRLLRNVAYIDDEDEEQEGAAQLDEMGLPVQRRRRRRQYED LENSDDDLLSDMDIDPLREELTLESLSNVKANSYSEWITQPNVSRTIARELKSFLLEYTDETGRSVYGARIRTLGEMNSE SLEVNYRHLAESKAILALFLAKCPEEMLKIFDLVAMEATELHYPDYARIHSEIHVRISDFPTIYSLRELRESNLSSLVRV TGVVTRRTGVFPQLKYVKFNCLKCGSILGPFFQDSNEEIRISFCTNCKSKGPFRVNGEKTVYRNYQRVTLQEAPGTVPPG RLPRHREVILLADLVDVSKPGEEVEVTGIYKNNYDGNLNAKNGFPVFATIIEANSIKRREGNTANEGEEGLDVFSWTEEE EREFRKISRDRGIIDKIISSMAPSIYGHRDIKTAVACSLFGGVPKNVNGKHSIRGDINVLLLGDPGTAKSQILKYVEKTA HRAVFATGQGASAVGLTASVRKDPITKEWTLEGGALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTTL QARCSIIAAANPNGGRYNSTLPLAQNVSLTEPILSRFDILCVVRDLVDEEADERLATFVVDSHVRSHPENDEDREGEELK NNGESAIEQGEDEINEQLNARQRRLQRQRKKEEEISPIPQELLMKYIHYARTKIYPKLHQMDMDKVSRVYADLRRESIST GSFPITVRHLESILRIAESFAKMRLSEFVSSYDLDRAIKVVVDSFVDAQKVSVRRQLRRSFAIYTLGH P29469 3.6.4.12 DNA replication licensing factor MCM3 Saccharomyces cerevisiae 0.107653508 2 Saccharomyces cerevisiae LEVO MEGSTGFDGDATTFFAPDAVFGDRVRRFQEFLDTFTSYRDSVRSIQVYNSNNAANYNDDQDDADERDLLGDDDGDDLEKE KKAASSTSLNILPHRIIISLDDLREFDRSFWSGILVEPAYFIPPAEKALTDLADSMDDVPHPNASAVSSRHPWKLSFKGS FGAHALSPRTLTAQHLNKLVSVEGIVTKTSLVRPKLIRSVHYAAKTGRFHYRDYTDATTTLTTRIPTPAIYPTEDTEGNK LTTEYGYSTFIDHQRITVQEMPEMAPAGQLPRSIDVILDDDLVDKTKPGDRVNVVGVFKSLGAGGMNQSNSNTLIGFKTL ILGNTVYPLHARSTGVAARQMLTDFDIRNINKLSKKKDIFDILSQSLAPSIYGHDHIKKAILLMLMGGVEKNLENGSHLR GDINILMVGDPSTAKSQLLRFVLNTASLAIATTGRGSSGVGLTAAVTTDRETGERRLEAGAMVLADRGVVCIDEFDKMTD VDRVAIHEVMEQQTVTIAKAGIHTTLNARCSVIAAANPVFGQYDVNRDPHQNIALPDSLLSRFDLLFVVTDDINEIRDRS ISEHVLRTHRYLPPGYLEGEPVRERLNLSLAVGEDADINPEEHSNSGAGVENEGEDDEDHVFEKFNPLLQAGAKLAKNKG NYNGTEIPKLVTIPFLRKYVQYAKERVIPQLTQEAINVIVKNYTDLRNDDNTKKSPITARTLETLIRLATAHAKVRLSKT VNKVDAKVAANLLRFALLGEDIGNDIDEEESEYEEALSKRSPQKSPKKRQRVRQPASNSGSPIKSTPRRSTASSVNATPS SARRILRFQDDEQNAGEDDNDIMSPLPADEEAELQRRLQLGLRVSPRRREHLHAPEEGSSGPLTEVGTPRLPNVSSAGQD DEQQQSVISFDNVEPGTISTGRLSLISGIIARLMQTEIFEEESYPVASLFERINEELPEEEKFSAQEYLAGLKIMSDRNN LMVADDKVWRV P24279 3.6.4.12 DNA replication licensing factor MCM4 Saccharomyces cerevisiae 0.10513837499999999 2 Saccharomyces cerevisiae LEVO MSQQSSSPTKEDNNSSSPVVPNPDSVPPQLSSPALFYSSSSSQGDIYGRNNSQNLSQGEGNIRAAIGSSPLNFPSSSQRQ NSDVFQSQGRQGRIRSSASASGRSRYHSDLRSDRALPTSSSSLGRNGQNRVHMRRNDIHTSDLSSPRRIVDFDTRSGVNT LDTSSSSAPPSEASEPLRIIWGTNVSIQECTTNFRNFLMSFKYKFRKILDEREEFINNTTDEELYYIKQLNEMRELGTSN LNLDARNLLAYKQTEDLYHQLLNYPQEVISIMDQTIKDCMVSLIVDNNLDYDLDEIETKFYKVRPYNVGSCKGMRELNPN DIDKLINLKGLVLRSTPVIPDMKVAFFKCNVCDHTMAVEIDRGVIQEPARCERIDCNEPNSMSLIHNRCSFADKQVIKLQ ETPDFVPDGQTPHSISLCVYDELVDSCRAGDRIEVTGTFRSIPIRANSRQRVLKSLYKTYVDVVHVKKVSDKRLDVDTST IEQELMQNKVDHNEVEEVRQITDQDLAKIREVAAREDLYSLLARSIAPSIYELEDVKKGILLQLFGGTNKTFTKGGRYRG DINILLCGDPSTSKSQILQYVHKITPRGVYTSGKGSSAVGLTAYITRDVDTKQLVLESGALVLSDGGVCCIDEFDKMSDS TRSVLHEVMEQQTISIAKAGIITTLNARSSILASANPIGSRYNPNLPVTENIDLPPPLLSRFDLVYLVLDKVDEKNDREL AKHLTNLYLEDKPEHISQDDVLPVEFLTMYISYAKEHIHPIITEAAKTELVRAYVGMRKMGDDSRSDEKRITATTRQLES MIRLAEAHAKMKLKNVVELEDVQEAVRLIRSAIKDYATDPKTGKIDMNLVQTGKSVIQRKLQEDLSREIMNVLKDQASDS MSFNELIKQINEHSQDRVESSDIQEALSRLQQEDKVIVLGEGVRRSVRLNNRV P30665 3.6.4.12 Minichromosome maintenance protein 5 Saccharomyces cerevisiae 0.08650573399999999 2 Saccharomyces cerevisiae LEVO MSFDRPEIYSAPVLQGESPNDDDNTEIIKSFKNFILEFRLDSQFIYRDQLRNNILVKNYSLTVNMEHLIGYNEDIYKKLS DEPSDIIPLFETAITQVAKRISILSRAQSANNNDKDPENTSMDTDSLLLNSLPTFQLILNSNANQIPLRDLDSEHVSKIV RLSGIIISTSVLSSRATYLSIMCRNCRHTTSITINNFNSITGNTVSLPRSCLSTIESESSMANESNIGDESTKKNCGPDP YIIIHESSKFIDQQFLKLQEIPELVPVGEMPRNLTMTCDRYLTNKVIPGTRVTIVGIYSIYNSKNGAGSGRSGGGNGGSG VAIRTPYIKILGIQSDVETSSIWNSVTMFTEEEEEEFLQLSRNPKLYEILTNSIAPSIFGNEDIKKAIVCLLMGGSKKIL PDGMRLRGDINVLLLGDPGTAKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVQRDPMTREFYLEGGAMVLADGGVVCID EFDKMRDEDRVAIHEAMEQQTISIAKAGITTVLNSRTSVLAAANPIYGRYDDLKSPGDNIDFQTTILSRFDMIFIVKDDH NEERDISIANHVINIHTGNANAMQNQQEENGSEISIEKMKRYITYCRLKCAPRLSPQAAEKLSSNFVTIRKQLLINELES TERSSIPITIRQLEAIIRITESLAKLELSPIAQERHVDEAIRLFQASTMDAASQDPIGGLNQASGTSLSEIRRFEQELKR RLPIGWSTSYQTLRREFVDTHRFSQLALDKALYALEKHETIQLRHQGQNIYRSGV P29496 3.6.4.12 DNA replication licensing factor MCM6 Saccharomyces cerevisiae 0.11311021099999999 2 Saccharomyces cerevisiae LEVO MSSPFPADTPSSNRPSNSSPPPSSIGAGFGSSSGLDSQIGSRLHFPSSSQPHVSNSQTGPFVNDSTQFSSQRLQTDGSAT NDMEGNEPARSFKSRALNHVKKVDDVTGEKVREAFEQFLEDFSVQSTDTGEVEKVYRAQIEFMKIYDLNTIYIDYQHLSM RENGALAMAISEQYYRFLPFLQKGLRRVVRKYAPELLNTSDSLKRSEGDEGQADEDEQQDDDMNGSSLPRDSGSSAAPGN GTSAMATRSITTSTSPEQTERVFQISFFNLPTVHRIRDIRSEKIGSLLSISGTVTRTSEVRPELYKASFTCDMCRAIVDN VEQSFKYTEPTFCPNPSCENRAFWTLNVTRSRFLDWQKVRIQENANEIPTGSMPRTLDVILRGDSVERAKPGDRCKFTGV EIVVPDVTQLGLPGVKPSSTLDTRGISKTTEGLNSGVTGLRSLGVRDLTYKISFLACHVISIGSNIGASSPDANSNNRET ELQMAANLQANNVYQDNERDQEVFLNSLSSDEINELKEMVKDEHIYDKLVRSIAPAVFGHEAVKKGILLQMLGGVHKSTV EGIKLRGDINICVVGDPSTSKSQFLKYVVGFAPRSVYTSGKASSAAGLTAAVVRDEEGGDYTIEAGALMLADNGICCIDE FDKMDISDQVAIHEAMEQQTISIAKAGIHATLNARTSILAAANPVGGRYNRKLSLRGNLNMTAPIMSRFDLFFVILDDCN EKIDTELASHIVDLHMKRDEAIEPPFSAEQLRRYIKYARTFKPILTKEARSYLVEKYKELRKDDAQGFSRSSYRITVRQL ESMIRLSEAIARANCVDEITPSFIAEAYDLLRQSIIRVDVDDVEMDEEFDNIESQSHAASGNNDDNDDGTGSGVITSEPP ADIEEGQSEATARPGTSEKKKTTVTYDKYVSMMNMIVRKIAEVDREGAEELTAVDIVDWYLLQKENDLGSLAEYWEERRL AFKVIKRLVKDRILMEIHGTRHNLRDLENEENENNKTVYVIHPNCEVLDQLEPQDSS P53091 3.6.4.12 DNA replication licensing factor MCM7 Saccharomyces cerevisiae 0.09504987499999999 2 Saccharomyces cerevisiae LEVO MSAALPSIQLPVDYNNLFNEITDFLVTFKQDTLSSDATRNENEDENLDAENIEQHLLEKGPKYMAMLQKVANRELNSVII DLDDILQYQNEKFLQGTQADDLVSAIQQNANHFTELFCRAIDNNMPLPTKEIDYKDDVLDVILNQRRLRNERMLSDRTNE IRSENLMDTTMDPPSSMNDALREVVEDETELFPPNLTRRYFLYFKPLSQNCARRYRKKAISSKPLSVRQIKGDFLGQLIT VRGIITRVSDVKPAVEVIAYTCDQCGYEVFQEVNSRTFTPLSECTSEECSQNQTKGQLFMSTRASKFSAFQECKIQELSQ QVPVGHIPRSLNIHVNGTLVRSLSPGDIVDVTGIFLPAPYTGFKALKAGLLTETYLEAQFVRQHKKKFASFSLTSDVEER VMELITSGDVYNRLAKSIAPEIYGNLDVKKALLLLLVGGVDKRVGDGMKIRGDINVCLMGDPGVAKSQLLKAICKISPRG VYTTGKGSSGVGLTAAVMKDPVTDEMILEGGALVLADNGICCIDEFDKMDESDRTAIHEVMEQQTISISKAGINTTLNAR TSILAAANPLYGRYNPRLSPLDNINLPAALLSRFDILFLMLDIPSRDDDEKLAEHVTYVHMHNKQPDLDFTPVEPSKMRE YIAYAKTKRPVMSEAVNDYVVQAYIRLRQDSKREMDSKFSFGQATPRTLLGIIRLSQALAKLRLADMVDIDDVEEALRLV RVSKESLYQETNKSKEDESPTTKIFTIIKKMLQETGKNTLSYENIVKTVRLRGFTMLQLSNCIQEYSYLNVWHLINEGNT LKFVDDGTMDTDQEDSLVSTPKLAPQTTASANVSAQDSDIDLQDA P38132 3.6.4.12 DNA replication regulator SLD3 Saccharomyces cerevisiae 0.077428633 1 Saccharomyces cerevisiae LEVO METWEVIASVKEATKGLDLSLDHPLIIKSEDVPSNILQLLQQKNRRQLKHICMKSRKEYFLLEEYGPGFWVKWPYNYFNG YSLPERRTEVVTTVERERAKRETLKTWDELKFKELLHLWSEEPKGSCKLEKDKDLKLDMNPPDMKGESKINDYYSDPKEY IESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKR KNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDFEKKYKLKLKKRSLNLTKKGLVRRRSK KKTSEKDKGIERITTSLDYCEQLDLYLDRACILDILLSSETPNPDAIEASNGTIQEHKKNILDKSKEASLVGFINYVLIP YFNKKVPHAVEFIIQKLKGPSMRPKRALKKVNDSTNVSSPNTVETYNRLSTSQRASRSSIINSVPSSPALRRVDANLFSR KSIASPTPELLNSRTNSNLNEFLESETRSLKRPSQLGRTKSDLTMNHLQKRQFSVSDLSTTRVPNSSTITLKTPFSHSTI NAYKTMNNSFRRVGKRKDINETIRLHERVDSEENVQVQATPAVKKRTVTPNKKAQLQSIIESPLNFKDDDTHEGRKNTSN ITSTPTNKPPENSSKRRVRRRLFAPEST P53135 Cell division control protein 45 Saccharomyces cerevisiae 0.07432483599999999 1 Saccharomyces cerevisiae LEVO MYYGISQFSEAYNKILRNSSSHSSCQLVIFVSCLNIDALCATKMLSLLFKKQLVQSQIVPIFGYSELRRHYSQLDDNINS LLLVGFGGVIDLEAFLEIDPQEYVIDTDEKSGEQSFRRDIYVLDAHRPWNLDNIFGSQIIQCFDDGTVDDTLGEQKEAYY KLLELDEESGDDELSGDENDNNGGDDEATDADEVTDEDEEDEDETISNKRGNSSIGPNDLSKRKQRKKQIHEYEGVLEEY YSQGTTVVNSISAQIYSLLSAIGETNLSNLWLNILGTTSLDIAYAQVYNRLYPLLQDEVKRLTPSSRNSVKTPDTLTLNI QPDYYLFLLRHSSLYDSFYYSNYVNAKLSLWNENGKKRLHKMFARMGIPLSTAQETWLYMDHSIKRELGIIFDKNLDRYG LQDIIRDGFVRTLGYRGSISASEFVEALTALLEVGNSTDKDSVKINNDNNDDTDGEEEEDNSAQKLTNLRKRWVSNFWLS WDALDDRKVELLNRGIQLAQDLQRAIFNTGVAILEKKLIKHLRIYRLCVLQDGPDLDLYRNPLTLLRLGNWLIECCAESE DKQLLPMVLASIDENTDTYLVAGLTPRYPRGLDTIHTKKPILNNFSMAFQQITAETDAKVRIDNFESSIIEIRREDLSPF LEKLTLSGLL Q08032 Mitochondrial morphogenesis protein SLD7 Saccharomyces cerevisiae 0.029598828 1 Saccharomyces cerevisiae LEVO MSRKLCTLNFTLSGKQGSLVIRDIQLWSNRPTASKSTSELRGQFIQYVDLAKLPLWVRSTNMNTYRCYSTSATAQAYFKS KLRNANRGIVIELFDKVDQRSQEPAYLIIFRENTELNCFQVDLTMKHEFDGQVTKLKQDIGKTRASVSKEGSIDIIIQQS QQRKIGTKTEVYRNVHINDKRLQFNETLSKLILGGLRLRGISNSITDYQKLYKITFDAAEFTHRDELKRISMGSGEEVSF ESLQETVETLLKLFTKS Q08457 ADENOSINE-5'-DIPHOSPHATE 0.000427201 8 ADP ZINC ION 6.5409e-05 10 ZN singleParticle particle 7.5 Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS 2.0 GLOW DISCHARGE 30 AIR 0.1 ETHANE 100 277 FEI VITROBOT MARK IV

Wait time: 30 s Blotting time: 1.5 s Blot force: +2.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 3.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN EPU FEI FALCON III (4k x 4k) INTEGRATING 1 10192 58.4 FEI FALCON III (4k x 4k) INTEGRATING 1 6046 62.1 1 CTFFIND 4.1.14 PHASE FLIPPING AND AMPLITUDE CORRECTION C2 2.9 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 RELION 4.0 post-process PHENIX 1.21.2-5419 phenix.combine_focused_maps

For the composite MSC map, resolution was estimated with phenix.mtriage, using the unmasked model-map FSC, which gave an FSC(0.143) resolution of 2.9 Angstrom. Final focused refinement particle subsets used to generate composite map (292,336 particles): DH core (38,859 particles) Sld3 MRD1/2:Mcm4/6 (149,668 particles) Sld3-Cdc45:Mcm2/5 (52,475 particles) Sld7:Mcm6 (51,334 particles)

292336 MAXIMUM LIKELIHOOD RELION 4.0 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 emd_55918.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 376 376 376 0 0 0 376 376 376 407.96002 407.96002 407.96002 90.0 90.0 90.0 X Y Z -16.284929999999999 32.615124000000002 0.005994572 0.9844461 1.085 1.085 1.085 4.61 AUTHOR ::::EMDATABANK.org::::EMD-55918:::: MCM2-7 DH-Sld3/7-Cdc45 (MSC) 7PT6 PDB experimental model 7P30 PDB experimental model 5BK4 PDB experimental model 3WI3 PDB experimental model 3X38 PDB experimental model 6U0M PDB experimental model