H. sapiens MCM bound to double stranded DNA and ORC6 as part of the MCM-ORC complex

2024-12-25 REL PDBe PDBe PDBe 2024-02-13 2024-10-02 2024-10-02 2024-12-25 The Francis Crick Institute CC2002, CC2009 United Kingdom European Research Council (ERC) 820102 European Union Wellcome Trust 219527/Z/19/Z United Kingdom European Research Council (ERC) 101020432-MeChroRep European Union H. sapiens MCM bound to double stranded DNA and ORC6 as part of the MCM-ORC complex Greiwe JF Weissmann F Diffley JFX Costa A AAA+ ATPase, DNA helicase, REPLICATION Weissmann F Greiwe JF Puhringer T Eastwood EL Couves EC Miller TCR Diffley JFX Costa A MCM double hexamer loading visualized with human proteins. Nature UK 636 499 508 2024 39604733 doi:10.1038/s41586-024-08263-6 1476-4687 0006 NATUAS Weissmann F Greiwe JF Puhringer T Miller TCR Diffley JFX Costa A MCM Double Hexamer Loading Visualised with Human Proteins Biorxiv US 2024 doi:10.1101/2024.04.10.588848 2692-8205 Liebschner D Afonine PV Baker ML Bunkoczi G Chen VB Croll TI Hintze B Hung LW Jain S McCoy AJ Moriarty NW Oeffner RD Poon BK Prisant MG Read RJ Richardson JS Richardson DC Sammito MD Sobolev OV Stockwell DH Terwilliger TC Urzhumtsev AG Videau LL Williams CJ Adams PD Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Acta Crystallogr., Sect. D: Biol. Crystallogr. DK 75 861 877 2019 31588918 doi:10.1107/S2059798319011471 0907-4449 0766 ABCRE6 EMD-19621 focused EM volume

Focused refinement of ORC1-5 in the MCM-ORC complex

EMD-19622 other EM volume

Composite map of the MCM-ORC complex (composed of the consensus map and the locally refined ORC1-5)

EMD-19618 other EM volume

Structure of the MCM double hexamer

EMD-19619 other EM volume

Structure of the MCM single hexamer bound to double stranded DNA

EMD-19625 other EM volume

Map of the MCM double hexamer containing the MCM5 AG mutation

EMD-19623 other EM volume

Structure of the OCCM complex

8s0b FULLOVERLAP H. sapiens MCM bound to double stranded DNA and ORC6 as part of the MCM-ORC complex H. sapiens MCM bound to double stranded DNA and ORC6 as part of the MCM-ORC complex 0 1 2 3 4 5 6 7 8 9 0.6 H. sapiens ORC6 1 1 Homo sapiens Double stranded DNA 1 8 9 synthetic construct H. sapiens MCM2-7 1 2 3 4 5 6 7 Homo sapiens Origin recognition complex subunit 6 Homo sapiens 0.028017696999999998 1 Escherichia coli LEVO GSELIGRLAPRLGLAEPDMLRKAEEYLRLSRVKCVGLSARTTETSSAVMCLDLAASWMKCPLDRAYLIKLSGLNKETYQS CLKSFECLLGLNSNIGIRDLAVQFSCIEAVNMASKILKSYESSLPQTQQVDLDLSRPLFTSAALLSACKILKLKVDKNKM VATSGVKKAIFDRLCKQLEKIGQQVDREPGDVATPPRKRKKIVVEAPAKEMEKVEEMPHKPQKDEDLTQDYEEWKRKILE NAASAQKATAE Q9Y5N6 DNA replication licensing factor MCM2 Homo sapiens 0.10203410199999999 1 Spodoptera frugiperda LEVO MAESSESFTMASSPAQRRRGNDPLTSSPGRSSRRTDALTSSPGRDLPPFEDESEGLLGTEGPLEEEEDGEELIGDGMERD YRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRDREAGRGLGRMRRGLLYDSDEEDEERPARKRRQVERATED GEEDEEMIESIENLEDLKGHSVREWVSMAGPRLEIHHRFKNFLRTHVDSHGHNVFKERISDMCKENRESLVVNYEDLAAR EHVLAYFLPEAPAELLQIFDEAALEVVLAMYPKYDRITNHIHVRISHLPLVEELRSLRQLHLNQLIRTSGVVTSCTGVLP QLSMVKYNCNKCNFVLGPFCQSQNQEVKPGSCPECQSAGPFEVNMEETIYQNYQRIRIQESPGKVAAGRLPRSKDAILLA DLVDSCKPGDEIELTGIYHNNYDGSLNTANGFPVFATVILANHVAKKDNKVAVGELTDEDVKMITSLSKDQQIGEKIFAS IAPSIYGHEDIKRGLALALFGGEPKNPGGKHKVRGDINVLLCGDPGTAKSQFLKYIEKVSSRAIFTTGQGASAVGLTAYV QRHPVSREWTLEAGALVLADRGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYDPS LTFSENVDLTEPIISRFDILCVVRDTVDPVQDEMLARFVVGSHVRHHPSNKEEEGLANGSAAEPAMPNTYGVEPLPQEVL KKYIIYAKERVHPKLNQMDQDKVAKMYSDLRKESMATGSIPITVRHIESMIRMAEAHARIHLRDYVIEDDVNMAIRVMLE SFIDTQKFSVMRSMRKTFARYLSFRRDNNELLLFILKQLVAEQVTYQRNRFGAQQDTIEVPEKDLVDKARQINIHNLSAF YDSELFRMNKFSHDLKRKMILQQF P49736 3.6.4.12 DNA replication licensing factor MCM3 Homo sapiens 0.09129702299999999 1 Spodoptera frugiperda LEVO GEMAGTVVLDDVELREAQRDYLDFLDDEEDQGIYQSKVRELISDNQYRLIVNVNDLRRKNEKRANRLLNNAFEELVAFQR ALKDFVASIDATYAKQYEEFYVGLEGSFGSKHVSPRTLTSCFLSCVVCVEGIVTKCSLVRPKVVRSVHYCPATKKTIERR YSDLTTLVAFPSSSVYPTKDEENNPLETEYGLSVYKDHQTITIQEMPEKAPAGQLPRSVDVILDDDLVDKAKPGDRVQVV GTYRCLPGKKGGYTSGTFRTVLIACNVKQMSKDAQPSFSAEDIAKIKKFSKTRSKDIFDQLAKSLAPSIHGHDYVKKAIL CLLLGGVERDLENGSHIRGDINILLIGDPSVAKSQLLRYVLCTAPRAIPTTGRGSSGVGLTAAVTTDQETGERRLEAGAM VLADRGVVCIDEFDKMSDMDRTAIHEVMEQGRVTIAKAGIHARLNARCSVLAAANPVYGRYDQYKTPMENIGLQDSLLSR FDLLFIMLDQMDPEQDREISDHVLRMHRYRAPGEQDGDAMPLGSAVDILATDDPNFSQEDQQDTQIYEKHDNLLHGTKKK KEKMVSAAFMKKYIHVAKIIKPVLTQESATYIAEEYSRLRSQDSMSSDTARTSPVTARTLETLIRLATAHAKARMSKTVD LQDAEEAVELVQYAYFKKVLEKEKKRKKRSEDESETEDEEEKSQEDQEQKRKRRKTRQPDAKDGDSYDPYDFSDTEEEMP QVHTPKTADSQETKESQKVELSESRLKAFKVALLDVFREAHAQSIGMNRLTESINRDSEEPFSSVEIQAALSKMQDDNQV MVSEGIIFLI P25205 3.6.4.12 DNA replication licensing factor MCM4 Homo sapiens 0.096702891 1 Spodoptera frugiperda LEVO MSSPASTPSRRGSRRGRATPAQTPRSEDARSSPSQRRRGEDSTSTGELQPMPTSPGVDLQSPAAQDVLFSSPPQMHSSAI PLDFDVSSPLTYGTPSSRVEGTPRSGVRGTPVRQRPDLGSAQKGLQVDLQSDGAAAEDIVASEQSLGQKLVIWGTDVNVA ACKENFQRFLQRFIDPLAKEEENVGIDITEPLYMQRLGEINVIGEPFLNVNCEHIKSFDKNLYRQLISYPQEVIPTFDMA VNEIFFDRYPDSILEHQIQVRPFNALKTKNMRNLNPEDIDQLITISGMVIRTSQLIPEMQEAFFQCQVCAHTTRVEMDRG RIAEPSVCGRCHTTHSMALIHNRSLFSDKQMIKLQESPEDMPAGQTPHTVILFAHNDLVDKVQPGDRVNVTGIYRAVPIR VNPRVSNVKSVYKTHIDVIHYRKTDAKRLHGLDEEAEQKLFSEKRVELLKELSRKPDIYERLASALAPSIYEHEDIKKGI LLQLFGGTRKDFSHTGRGKFRAEINILLCGDPGTSKSQLLQYVYNLVPRGQYTSGKGSSAVGLTAYVMKDPETRQLVLQT GALVLSDNGICCIDEFDKMNESTRSVLHEVMEQQTLSIAKAGIICQLNARTSVLAAANPIESQWNPKKTTIENIQLPHTL LSRFDLIFLMLDPQDEAYDRRLAHHLVALYYQSEEQAEEELLDMAVLKDYIAYAHSTIMPRLSEEASQALIEAYVDMRKI GSSRGMVSAYPRQLESLIRLAEAHAKVRLSNKVEAIDVEEAKRLHREALKQSATDPRTGIVDISILTTGMSATSRKRKEE LAEALKKLILSKGKTPALKYQQLFEDIRGQSDIAITKDMFEEALRALADDDFLTVTGKTVRLL P33991 3.6.4.12 DNA replication licensing factor MCM5 Homo sapiens 0.08240663299999999 1 Spodoptera frugiperda LEVO MSGFDDPGIFYSDSFGGDAQADEGQARKSQLQRRFKEFLRQYRVGTDRTGFTFKYRDELKRHYNLGEYWIEVEMEDLASF DEDLADYLYKQPAEHLQLLEEAAKEVADEVTRPRPSGEEVLQDIQVMLKSDASPSSIRSLKSDMMSHLVKIPGIIIAASA VRAKATRISIQCRSCRNTLTNIAMRPGLEGYALPRKCNTDQAGRPKCPLDPYFIMPDKCKCVDFQTLKLQELPDAVPHGE MPRHMQLYCDRYLCDKVVPGNRVTIMGIYSIKKFGLTTSRGRDRVGVGIRSSYIRVLGIQVDTDGSGRSFAGAVSPQEEE EFRRLAALPNVYEVISKSIAPSIFGGTDMKKAIACLLFGGSRKRLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPI GVYTSGKGSSAAGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNS RCSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVEGEIDLAKLK KFIAYCRVKCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAEALSKMKLQPFATEADVEEA LRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSEHSIIKDFTKQKYPEHAIHKVLQLMLRRGE IQHRMQRKVLYRLK P33992 3.6.4.12 DNA replication licensing factor MCM6 Homo sapiens 0.09301027299999999 1 Spodoptera frugiperda LEVO MDLAAAAEPGAGSQHLEVRDEVAEKCQKLFLDFLEEFQSSDGEIKYLQLAEELIRPERNTLVVSFVDLEQFNQQLSTTIQ EEFYRVYPYLCRALKTFVKDRKEIPLAKDFYVAFQDLPTRHKIRELTSSRIGLLTRISGQVVRTHPVHPELVSGTFLCLD CQTVIRDVEQQFKYTQPNICRNPVCANRRRFLLDTNKSRFVDFQKVRIQETQAELPRGSIPRSLEVILRAEAVESAQAGD KCDFTGTLIVVPDVSKLSTPGARAETNSRVSGVDGYETEGIRGLRALGVRDLSYRLVFLACCVAPTNPRFGGKELRDEEQ TAESIKNQMTVKEWEKVFEMSQDKNLYHNLCTSLFPTIHGNDEVKRGVLLMLFGGVPKTTGEGTSLRGDINVCIVGDPST AKSQFLKHVEEFSPRAVYTSGKASSAAGLTAAVVRDEESHEFVIEAGALMLADNGVCCIDEFDKMDVRDQVAIHEAMEQQ TISITKAGVKATLNARTSILAAANPISGHYDRSKSLKQNINLSAPIMSRFDLFFILVDECNEVTDYAIARRIVDLHSRIE ESIDRVYSLDDIRRYLLFARQFKPKISKESEDFIVEQYKHLRQRDGSGVTKSSWRITVRQLESMIRLSEAMARMHCCDEV QPKHVKEAFRLLNKSIIRVETPDVNLDQEEEIQMEVDEGAGGINGHADSPAPVNGINGYNEDINQESAPKASLRLGFSEY CRISNLIVLHLRKVEEEEDESALKRSELVNWYLKEIESEIDSEEELINKKRIIEKVIHRLTHYDHVLIELTQAGLKGSTE GSESYEEDPYLVVNPNYLLED Q14566 3.6.4.12 DNA replication licensing factor MCM7 Homo sapiens 0.081411875 1 Spodoptera frugiperda LEVO MALKDYALEKEKVKKFLQEFYQDDELGKKQFKYGNQLVRLAHREQVALYVDLDDVAEDDPELVDSICENARRYAKLFADA VQELLPQYKEREVVNKDVLDVYIEHRLMMEQRSRDPGMVRSPQNQYPAELMRRFELYFQGPSSNKPRVIREVRADSVGKL VTVRGIVTRVSEVKPKMVVATYTCDQCGAETYQPIQSPTFMPLIMCPSQECQTNRSGGRLYLQTRGSRFIKFQEMKMQEH SDQVPVGNIPRSITVLVEGENTRIAQPGDHVSVTGIFLPILRTGFRQVVQGLLSETYLEAHRIVKMNKSEDDESGAGELT REELRQIAEEDFYEKLAASIAPEIYGHEDVKKALLLLLVGGVDQSPRGMKIRGNINICLMGDPGVAKSQLLSYIDRLAPR SQYTTGRGSSGVGLTAAVLRDSVSGELTLEGGALVLADQGVCCIDEFDKMAEADRTAIHEVMEQQTISIAKAGILTTLNA RCSILAAANPAYGRYNPRRSLEQNIQLPAALLSRFDLLWLIQDRPDRDNDLRLAQHITYVHQHSRQPPSQFEPLDMKLMR RYIAMCREKQPMVPESLADYITAAYVEMRREAWASKDATYTSARTLLAILRLSTALARLRMVDVVEKEDVNEAIRLMEMS KDSLLGDKGQTARTQRPADVIFATVRELVSGGRSVRFSEAEQRCVSRGFTPAQFQAALDEYEELNVWQVNASRTRITFV P33993 3.6.4.12 DNA (45-mer) synthetic construct 0.013837882999999999 1 (DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DA)(DC)(DT)(DA)(DT)(DG)(DC)(DA) (DT)(DG)(DC)(DA)(DT)(DG)(DC)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG) (DC)(DA)(DT)(DG)(DC) DNA DNA (45-mer) synthetic construct 0.013877905 1 (DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DG)(DC) (DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DA)(DG)(DT)(DT)(DC)(DA)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DA)(DG) DNA PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER 0.0005232469999999999 3 AGS MAGNESIUM ION 2.4305e-05 6 MG ZINC ION 6.5409e-05 5 ZN ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP singleParticle particle 7.5 UltrAuFoil R1.2/1.3 GOLD 300 GRAPHENE OXIDE ETHANE 90 295 FEI VITROBOT MARK IV

The MCM recruitment reaction was reconstituted in vitro using purified H. sapiens proteins, a short DNA template and ATPgammaS. Four microlitres of the entire reaction was applied on a grid and incubated for 1 min at room temperature before blotting with filter paper for 5 s and plunge-freezing in liquid ethane.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 130000.0 NITROGEN GIF Bioquantum GATAN K2 SUMMIT (4k x 4k) COUNTING 1 31569 9.4 49.28 1 3.6 FSC 0.143 CUT-OFF 182341 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_19620.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.8916352 1.3037512 0.0026058783 0.02668206 1.08 1.08 1.08 0.17 AUTHOR ::::EMDATABANK.org::::EMD-19620:::: Consensus map of the human ORC bound to the amino-terminal side of a DNA-loaded MCM hexamer. The complex is referred to as MO*. Other experimental model

Model of the DNA-bound MCM hexamer that was determined in the same dataset.

AF-Q9Y5N6-F1 F AlphaFold in silico model emd_19620_msk_1.map emd_19620_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.7762855 1.245 0.0026007968 0.029424407 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-19620:::: Local refinement of the MCM2-7 in the MCM-ORC complex. emd_19620_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.32491466 0.7500535 0.001661095 0.034039482 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-19620:::: Half map 1 of the main map emd_19620_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.36503455 0.7908525 0.0016679529 0.034121316 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-19620:::: Half map 2 of the main map