Cryo-EM structure of human CMG helicase stalled at G4-containing DNA template

2025-03-26 REL RCSB INITIAL_RELEASE REPOSITORY RCSB RCSB 2024-10-23 2025-03-26 2025-03-26 2025-03-26 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM152094 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM126907 United States National Institutes of Health/National Cancer Institute (NIH/NCI) P30 CA008748 United States Cryo-EM structure of human CMG helicase stalled at G4-containing DNA template Allwein B Batra S Remus D Hite R helicase, DNA replication, cell division, fork stalling, translocation, REPLICATION, REPLICATION-DNA complex Batra S Allwein B Kumar C Devbhandari S Bruning JG Bahng S Lee CM Marians KJ Hite RK Remus D G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation. Science US 387 eadt1978 eadt1978 2025 40048517 doi:10.1126/science.adt1978 1095-9203 0038 SCIEAS EMD-47747 focused EM volume EMD-47748 focused EM volume EMD-47749 focused EM volume EMD-47916 consensus EM volume 9e2z FULLOVERLAP Human CMG, G4 stall state Human CMG, G4 stall state 0 7 8 9 10 11 12 13 2 5 4 1 3 6

Human CMG stalled at G4-containing DNA template, lacking the fork protection complex (TIMELESS-TIPIN)

Saccharomyces cerevisiae W303 0.58601 DNA replication licensing factor MCM2 Homo sapiens 0.10203410199999999 1 Trichoplusia ni LEVO MAESSESFTMASSPAQRRRGNDPLTSSPGRSSRRTDALTSSPGRDLPPFEDESEGLLGTEGPLEEEEDGEELIGDGMERD YRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRDREAGRGLGRMRRGLLYDSDEEDEERPARKRRQVERATED GEEDEEMIESIENLEDLKGHSVREWVSMAGPRLEIHHRFKNFLRTHVDSHGHNVFKERISDMCKENRESLVVNYEDLAAR EHVLAYFLPEAPAELLQIFDEAALEVVLAMYPKYDRITNHIHVRISHLPLVEELRSLRQLHLNQLIRTSGVVTSCTGVLP QLSMVKYNCNKCNFVLGPFCQSQNQEVKPGSCPECQSAGPFEVNMEETIYQNYQRIRIQESPGKVAAGRLPRSKDAILLA DLVDSCKPGDEIELTGIYHNNYDGSLNTANGFPVFATVILANHVAKKDNKVAVGELTDEDVKMITSLSKDQQIGEKIFAS IAPSIYGHEDIKRGLALALFGGEPKNPGGKHKVRGDINVLLCGDPGTAKSQFLKYIEKVSSRAIFTTGQGASAVGLTAYV QRHPVSREWTLEAGALVLADRGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYDPS LTFSENVDLTEPIISRFDILCVVRDTVDPVQDEMLARFVVGSHVRHHPSNKEEEGLANGSAAEPAMPNTYGVEPLPQEVL KKYIIYAKERVHPKLNQMDQDKVAKMYSDLRKESMATGSIPITVRHIESMIRMAEAHARIHLRDYVIEDDVNMAIRVMLE SFIDTQKFSVMRSMRKTFARYLSFRRDNNELLLFILKQLVAEQVTYQRNRFGAQQDTIEVPEKDLVDKARQINIHNLSAF YDSELFRMNKFSHDLKRKMILQQF P49736 3.6.4.12 Isoform 2 of DNA replication licensing factor MCM3 Homo sapiens 0.09604332 1 Trichoplusia ni LEVO MLPRSPPLPRGNLWWREEFGSFRAGVESSWEPPRDFGGGSSLAAGMAGTVVLDDVELREAQRDYLDFLDDEEDQGIYQSK VRELISDNQYRLIVNVNDLRRKNEKRANRLLNNAFEELVAFQRALKDFVASIDATYAKQYEEFYVGLEGSFGSKHVSPRT LTSCFLSCVVCVEGIVTKCSLVRPKVVRSVHYCPATKKTIERRYSDLTTLVAFPSSSVYPTKDEENNPLETEYGLSVYKD HQTITIQEMPEKAPAGQLPRSVDVILDDDLVDKAKPGDRVQVVGTYRCLPGKKGGYTSGTFRTVLIACNVKQMSKDAQPS FSAEDIAKIKKFSKTRSKDIFDQLAKSLAPSIHGHDYVKKAILCLLLGGVERDLENGSHIRGDINILLIGDPSVAKSQLL RYVLCTAPRAIPTTGRGSSGVGLTAAVTTDQETGERRLEAGAMVLADRGVVCIDEFDKMSDMDRTAIHEVMEQGRVTIAK AGIHARLNARCSVLAAANPVYGRYDQYKTPMENIGLQDSLLSRFDLLFIMLDQMDPEQDREISDHVLRMHRYRAPGEQDG DAMPLGSAVDILATDDPNFSQEDQQDTQIYEKHDNLLHGTKKKKEKMVSAAFMKKYIHVAKIIKPVLTQESATYIAEEYS RLRSQDSMSSDTARTSPVTARTLETLIRLATAHAKARMSKTVDLQDAEEAVELVQYAYFKKVLEKEKKRKKRSEDESETE DEEEKSQEDQEQKRKRRKTRQPDAKDGDSYDPYDFSDTEEEMPQVHTPKTADSQETKESQKVELSESRLKAFKVALLDVF REAHAQSIGMNRLTESINRDSEEPFSSVEIQAALSKMQDDNQVMVSEGIIFLI P25205 3.6.4.12 DNA replication licensing factor MCM4 Homo sapiens 0.09911946099999999 1 Trichoplusia ni LEVO MHHHHHHHHENLYFQGSSATMSSPASTPSRRGSRRGRATPAQTPRSEDARSSPSQRRRGEDSTSTGELQPMPTSPGVDLQ SPAAQDVLFSSPPQMHSSAIPLDFDVSSPLTYGTPSSRVEGTPRSGVRGTPVRQRPDLGSAQKGLQVDLQSDGAAAEDIV ASEQSLGQKLVIWGTDVNVAACKENFQRFLQRFIDPLAKEEENVGIDITEPLYMQRLGEINVIGEPFLNVNCEHIKSFDK NLYRQLISYPQEVIPTFDMAVNEIFFDRYPDSILEHQIQVRPFNALKTKNMRNLNPEDIDQLITISGMVIRTSQLIPEMQ EAFFQCQVCAHTTRVEMDRGRIAEPSVCGRCHTTHSMALIHNRSLFSDKQMIKLQESPEDMPAGQTPHTVILFAHNDLVD KVQPGDRVNVTGIYRAVPIRVNPRVSNVKSVYKTHIDVIHYRKTDAKRLHGLDEEAEQKLFSEKRVELLKELSRKPDIYE RLASALAPSIYEHEDIKKGILLQLFGGTRKDFSHTGRGKFRAEINILLCGDPGTSKSQLLQYVYNLVPRGQYTSGKGSSA VGLTAYVMKDPETRQLVLQTGALVLSDNGICCIDEFDKMNESTRSVLHEVMEQQTLSIAKAGIICQLNARTSVLAAANPI ESQWNPKKTTIENIQLPHTLLSRFDLIFLLLDPQDEAYDRRLAHHLVALYYQSEEQAEEELLDMAVLKDYIAYAHSTIMP RLSEEASQALIEAYVDMRKIGSSRGMVSAYPRQLESLIRLAEAHAKVRLSNKVEAIDVEEAKRLHREALKQSATDPRTGI VDISILTTGMSATSRKRKEELAEALKKLILSKGKTPALKYQQLFEDIRGQSDIAITKDMFEEALRALADDDFLTVTGKTV RLL P33991 3.6.4.12 DNA replication licensing factor MCM5 Homo sapiens 0.08240663299999999 1 Trichoplusia ni 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 Trichoplusia ni 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 Trichoplusia ni LEVO MALKDYALEKEKVKKFLQEFYQDDELGKKQFKYGNQLVRLAHREQVALYVDLDDVAEDDPELVDSICENARRYAKLFADA VQELLPQYKEREVVNKDVLDVYIEHRLMMEQRSRDPGMVRSPQNQYPAELMRRFELYFQGPSSNKPRVIREVRADSVGKL VTVRGIVTRVSEVKPKMVVATYTCDQCGAETYQPIQSPTFMPLIMCPSQECQTNRSGGRLYLQTRGSRFIKFQEMKMQEH SDQVPVGNIPRSITVLVEGENTRIAQPGDHVSVTGIFLPILRTGFRQVVQGLLSETYLEAHRIVKMNKSEDDESGAGELT REELRQIAEEDFYEKLAASIAPEIYGHEDVKKALLLLLVGGVDQSPRGMKIRGNINICLMGDPGVAKSQLLSYIDRLAPR SQYTTGRGSSGVGLTAAVLRDSVSGELTLEGGALVLADQGVCCIDEFDKMAEADRTAIHEVMEQQTISIAKAGILTTLNA RCSILAAANPAYGRYNPRRSLEQNIQLPAALLSRFDLLWLIQDRPDRDNDLRLAQHITYVHQHSRQPPSQFEPLDMKLMR RYIAMCREKQPMVPESLADYITAAYVEMRREAWASKDATYTSARTLLAILRLSTALARLRMVDVVEKEDVNEAIRLMEMS KDSLLGDKGQTARTQRPADVIFATVRELVSGGRSVRFSEAEQRCVSRGFTPAQFQAALDEYEELNVWQVNASRTRITFV P33993 3.6.4.12 DNA replication complex GINS protein PSF1 Homo sapiens 0.023022469 1 Trichoplusia ni LEVO MFCEKAMELIRELHRAPEGQLPAFNEDGLRQVLEEMKALYEQNQSDVNEAKSGGRSDLIPTIKFRHCSLLRNRRCTVAYL YDRLLRIRALRWEYGSVLPNALRFHMAAEEMEWFNNYKRSLATYMRSLGGDEGLDITQDMKPPKSLYIEVRCLKDYGEFE VDDGTSVLLKKNSQHFLPRWKCEQLIRQGVLEHILS Q14691 DNA replication complex GINS protein PSF2 Homo sapiens 0.025336793 1 Trichoplusia ni LEVO MDAAEVEFLAEKELVTIIPNFSLDKIYLIGGDLGPFNPGLPVEVPLWLAINLKQRQKCRLLPPEWMDVEKLEKMRDHERK EETFTPMPSPYYMELTKLLLNHASDNIPKADEIRTLVKDMWDTRIAKLRVSADSFVRQQEAHAKLDNLTLMEINTSGTFL TQALNHMYKLRTNLQPLESTQSQDFENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK Q9Y248 DNA replication complex GINS protein PSF3 Homo sapiens 0.024562610999999998 1 Trichoplusia ni LEVO MSEAYFRVESGALGPEENFLSLDDILMSHEKLPVRTETAMPRLGAFFLERSAGAETDNAVPQGSKLELPLWLAKGLFDNK RRILSVELPKIYQEGWRTVFSADPNVVDLHKMGPHFYGFGSQLLHFDSPENADISQSLLQTFIGRFRRIMDSSQNAYNED TSALVARLDEMERGLFQTGQKGLNDFQCWEKGQASQITASNLVQNYKKRKFTDMED Q9BRX5 DNA replication complex GINS protein SLD5 Homo sapiens 0.026081873 1 Trichoplusia ni LEVO MTEEVDFLGQDSDGGSEEVVLTPAELIERLEQAWMNEKFAPELLESKPEIVECVMEQLEHMEENLRRAKREDLKVSIHQM EMERIRYVLSSYLRCRLMKIEKFFPHVLEKEKTRPEGEPSSLSPEELAFAREFMANTESYLKNVALKHMPPNLQKVDLFR AVPKPDLDSYVFLRVRERQENILVEPDTDEQRDYVIDLEKGSQHLIRYKTIAPLVASGAVQLI Q9BRT9 Cell division control protein 45 homolog Homo sapiens 0.065651539 1 Trichoplusia ni LEVO MFVSDFRKEFYEVVQSQRVLLFVASDVDALCACKILQALFQCDHVQYTLVPVSGWQELETAFLEHKEQFHYFILINCGAN VDLLDILQPDEDTIFFVCDTHRPVNVVNVYNDTQIKLLIKQDDDLEVPAYEDIFRDEEEDEEHSGNDSDGSEPSEKRTRL EEEIVEQTMRRRQRREWEARRRDILFDYEQYEYHGTSSAMVMFELAWMLSKDLNDMLWWAIVGLTDQWVQDKITQMKYVT DVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYDLRLVLYQHWSLHDSLCNTSYTAARFKLWSVHGQKRLQEFLADMGL PLKQVKQKFQAMDISLKENLREMIEESANKFGMKDMRVQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQA LDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTNLVISQGPFLYCSLMEGTPDVMLFSRPASLSLLSKHLLKSFVCS TKNRRCKLLPLVMAAPLSMEHGTVTVVGIPPETDSSDRKNFFGRAFEKAAESTSSRMLHNHFDLSVIELKAEDRSKFLDA LISLLS O75419 Leading strand DNA template synthetic construct 0.012582038 1 (DG)(DT)(DG)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DC)(DT)(DT)(DT)(DG)(DG)(DG)(DT)(DG)(DG) (DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DT)(DG)(DA)(DG)(DG)(DC)(DA)(DA)(DT)(DA) DNA Lagging strand DNA template synthetic construct 0.003968626 1 (DA)(DA)(DG)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DC) DNA ADENOSINE-5'-DIPHOSPHATE 0.000427201 1 ADP MAGNESIUM ION 2.4305e-05 6 MG ADENOSINE-5'-TRIPHOSPHATE 0.000507181 5 ATP ZINC ION 6.5409e-05 4 ZN POTASSIUM ION 3.9098e-05 2 K water 1.8015e-05 39 HOH singleParticle particle .01 7.6 20.0 C8H17KN2O4S HEPES-KOH 100.0 CH3CO2K Potassium acetate 10.0 Mg(CH3COO)2 Magnesium acetate 2.5 C4H10O2S2 DTT 0.02 H(C2H4O)nO(C6H4)C9H19 NP-40S 100.0 C10H17N6O12P3 AMP-PNP 5.0 C10H16N5O13P3 ATP Quantifoil R1.2/1.3 GOLD 400 GRAPHENE OXIDE CONTINUOUS 0.5 ETHANE 95 277 FEI VITROBOT MARK IV

30 second wait time after sample application; 30 second blot time, blot force 0.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 1.8 29000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 3325 3.0 66.0 1 1587336 C1 2.6 FSC 0.143 CUT-OFF cryoSPARC 4.0.0 187345 OTHER cryoSPARC 4.0.0

Stochastic gradient descent (cryoSPARC ab initio model generation)

MAXIMUM LIKELIHOOD cryoSPARC 4.0.0 cryoSPARC 4.0.0 emd_47473.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 370.04797 370.04797 370.04797 90.0 90.0 90.0 Z Y X -39.674550000000004 100.950019999999995 0.0073895156 1.3309585 0.8259999 0.8259999 0.8259999 3.0 AUTHOR ::::EMDATABANK.org::::EMD-47473:::: Composite Map Other in silico model

ModelAngelo

AB INITIO MODEL

Initial fitting was performed de novo by ModelAngelo, then iteratively improved with ChimeraX/ISOLDE, Coot, and Phenix real-space refinement algorithms.

REAL 49.990000000000002 emd_47473_msk_1.map