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- EMDB-55918: Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55918
TitleCryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (composite map)
Map dataMCM2-7 DH-Sld3/7-Cdc45 (MSC)
Sample
  • Complex: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
    • DNA: x 2 types
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsHelicase / Activation / Phosphorylation / REPLICATION
Function / homology
Function and homology information


regulation of mitotic DNA replication initiation / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / MCM complex binding / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex ...regulation of mitotic DNA replication initiation / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / MCM complex binding / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / single-stranded DNA helicase activity / mitotic DNA replication checkpoint signaling / MCM complex / mitotic DNA replication initiation / mitotic DNA replication / silent mating-type cassette heterochromatin formation / double-strand break repair via break-induced replication / DNA strand elongation involved in DNA replication / nuclear replication fork / DNA replication origin binding / subtelomeric heterochromatin formation / chromosome, centromeric region / DNA replication initiation / regulation of DNA-templated DNA replication initiation / helicase activity / transcription elongation by RNA polymerase II / nuclear envelope / peroxisome / single-stranded DNA binding / spindle pole / heterochromatin formation / DNA helicase / DNA replication / DNA helicase activity / chromosome, telomeric region / chromatin binding / DNA damage response / chromatin / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitochondrial morphogenesis protein Sld7 / Sld7 C-terminal domain / Sld7, N-terminal / Sld7 C-terminal domain / Mitochondrial morphogenesis protein SLD7 N-terminal domain / Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain ...Mitochondrial morphogenesis protein Sld7 / Sld7 C-terminal domain / Sld7, N-terminal / Sld7 C-terminal domain / Mitochondrial morphogenesis protein SLD7 N-terminal domain / Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain / CDC45 family / CDC45 / : / MCM3 winged helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / : / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm3 / : / MCM3-like, winged helix domain / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family C-terminal AAA(+) ATPase domain (MCM-CTD) profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM6 / DNA replication regulator SLD3 / Cell division control protein 45 / Mitochondrial morphogenesis protein SLD7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSaleh A / Noguchi Y / Schneider S / Aramayo R / Speck C
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust107903/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T005378/1 United Kingdom
Cancer Research UKDRCNPG-May21/100006 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural insights into Sld3-Sld7-dependent Cdc45 loading during replication initiation.
Authors: Yasunori Noguchi / Almutasem Saleh / Sarah Schneider / Marina E Ivanova / Zhuo Angel Chen / Lepakshi Ranjha / Ricardo Aramayo / Silvia Tognetti / Sarah V Faull / Juri Rappsilber / Christian Speck /
Abstract: Regulated helicase activation by DDK kinase is central for genome stability. However, how DDK phosphorylation primes the MCM2-7 double hexamer (DH) for Sld3-Sld7 binding and Cdc45 loading remained ...Regulated helicase activation by DDK kinase is central for genome stability. However, how DDK phosphorylation primes the MCM2-7 double hexamer (DH) for Sld3-Sld7 binding and Cdc45 loading remained unclear. We define this mechanism through cryo-EM structures of MCM2-7 DH-Sld3-Sld7 (MS) and MCM2-7 DH-Sld3-Sld7-Cdc45 (MSC). We reveal that the autoinhibitory Mcm4 tail engages not only Mcm4 but also Mcm6. Upon DDK-dependent phosphorylation, both of these sites become accessible. In the context of the MS structure, we identify that two short Sld3 motifs that contact Mcm4 and Mcm6 read out the DH phosphorylation state, while the Sld3 Treslin domain (STD) binds to Mcm2. In the MSC structure, Cdc45 dislodges the Sld3 STD from Mcm2, allowing Sld3 to position Cdc45 at the Mcm2/Mcm5 interface. Mutagenesis of the Sld3 STD-Cdc45 interface disrupts Cdc45 loading, validating this interaction. Together, our data reveal a phosphorylation-encoded mechanism coupling DDK-activated Mcm4/Mcm6 surfaces to distal Cdc45 placement, explaining how firing factors choreograph the DH-to-CMG transition.
History
DepositionDec 3, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55918.png

Downloads & links

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Map

FileDownload / File: emd_55918.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMCM2-7 DH-Sld3/7-Cdc45 (MSC)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 376 pix.
= 407.96 Å		1.09 Å/pix.
x 376 pix.
= 407.96 Å		1.09 Å/pix.
x 376 pix.
= 407.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.61
Minimum - Maximum-16.284929999999999 - 32.615124000000002
Average (Standard dev.)0.005994572 (±0.9844461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 407.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

EntireName: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
Components
  • Complex: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
    • DNA: dsDNA (60-MER)
    • DNA: dsDNA (60-MER)
    • Protein or peptide: DNA replication licensing factor MCM2
    • Protein or peptide: DNA replication licensing factor MCM3
    • Protein or peptide: DNA replication licensing factor MCM4
    • Protein or peptide: Minichromosome maintenance protein 5
    • Protein or peptide: DNA replication licensing factor MCM6
    • Protein or peptide: DNA replication licensing factor MCM7
    • Protein or peptide: DNA replication regulator SLD3
    • Protein or peptide: Cell division control protein 45
    • Protein or peptide: Mitochondrial morphogenesis protein SLD7
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

SupramoleculeName: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 1.65 MDa

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Macromolecule #1: dsDNA (60-MER)

MacromoleculeName: dsDNA (60-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.491848 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #2: dsDNA (60-MER)

MacromoleculeName: dsDNA (60-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.491848 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #3: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 98.911539 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDNRRRRRE EDDSDSENEL PPSSPQQHFR GGMNPVSSPI GSPDMINPEG DDNEVDDVPD IDEVEEQMNE VDLMDDNMYE DYAADHNRD RYDPDQVDDR EQQELSLSER RRIDAQLNER DRLLRNVAYI DDEDEEQEGA AQLDEMGLPV QRRRRRRQYE D LENSDDDL ...String:
MSDNRRRRRE EDDSDSENEL PPSSPQQHFR GGMNPVSSPI GSPDMINPEG DDNEVDDVPD IDEVEEQMNE VDLMDDNMYE DYAADHNRD RYDPDQVDDR EQQELSLSER RRIDAQLNER DRLLRNVAYI DDEDEEQEGA AQLDEMGLPV QRRRRRRQYE D LENSDDDL LSDMDIDPLR EELTLESLSN VKANSYSEWI TQPNVSRTIA RELKSFLLEY TDETGRSVYG ARIRTLGEMN SE SLEVNYR HLAESKAILA LFLAKCPEEM LKIFDLVAME ATELHYPDYA RIHSEIHVRI SDFPTIYSLR ELRESNLSSL VRV TGVVTR RTGVFPQLKY VKFNCLKCGS ILGPFFQDSN EEIRISFCTN CKSKGPFRVN GEKTVYRNYQ RVTLQEAPGT VPPG RLPRH REVILLADLV DVSKPGEEVE VTGIYKNNYD GNLNAKNGFP VFATIIEANS IKRREGNTAN EGEEGLDVFS WTEEE EREF RKISRDRGII DKIISSMAPS IYGHRDIKTA VACSLFGGVP KNVNGKHSIR GDINVLLLGD PGTAKSQILK YVEKTA HRA VFATGQGASA VGLTASVRKD PITKEWTLEG GALVLADKGV CLIDEFDKMN DQDRTSIHEA MEQQSISISK AGIVTTL QA RCSIIAAANP NGGRYNSTLP LAQNVSLTEP ILSRFDILCV VRDLVDEEAD ERLATFVVDS HVRSHPENDE DREGEELK N NGESAIEQGE DEINEQLNAR QRRLQRQRKK EEEISPIPQE LLMKYIHYAR TKIYPKLHQM DMDKVSRVYA DLRRESIST GSFPITVRHL ESILRIAESF AKMRLSEFVS SYDLDRAIKV VVDSFVDAQK VSVRRQLRRS FAIYTLGH

UniProtKB: DNA replication licensing factor MCM2

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Macromolecule #4: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 107.653508 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEGSTGFDGD ATTFFAPDAV FGDRVRRFQE FLDTFTSYRD SVRSIQVYNS NNAANYNDDQ DDADERDLLG DDDGDDLEKE KKAASSTSL NILPHRIIIS LDDLREFDRS FWSGILVEPA YFIPPAEKAL TDLADSMDDV PHPNASAVSS RHPWKLSFKG S FGAHALSP ...String:
MEGSTGFDGD ATTFFAPDAV FGDRVRRFQE FLDTFTSYRD SVRSIQVYNS NNAANYNDDQ DDADERDLLG DDDGDDLEKE KKAASSTSL NILPHRIIIS LDDLREFDRS FWSGILVEPA YFIPPAEKAL TDLADSMDDV PHPNASAVSS RHPWKLSFKG S FGAHALSP RTLTAQHLNK LVSVEGIVTK TSLVRPKLIR SVHYAAKTGR FHYRDYTDAT TTLTTRIPTP AIYPTEDTEG NK LTTEYGY STFIDHQRIT VQEMPEMAPA GQLPRSIDVI LDDDLVDKTK PGDRVNVVGV FKSLGAGGMN QSNSNTLIGF KTL ILGNTV YPLHARSTGV AARQMLTDFD IRNINKLSKK KDIFDILSQS LAPSIYGHDH IKKAILLMLM GGVEKNLENG SHLR GDINI LMVGDPSTAK SQLLRFVLNT ASLAIATTGR GSSGVGLTAA VTTDRETGER RLEAGAMVLA DRGVVCIDEF DKMTD VDRV AIHEVMEQQT VTIAKAGIHT TLNARCSVIA AANPVFGQYD VNRDPHQNIA LPDSLLSRFD LLFVVTDDIN EIRDRS ISE HVLRTHRYLP PGYLEGEPVR ERLNLSLAVG EDADINPEEH SNSGAGVENE GEDDEDHVFE KFNPLLQAGA KLAKNKG NY NGTEIPKLVT IPFLRKYVQY AKERVIPQLT QEAINVIVKN YTDLRNDDNT KKSPITARTL ETLIRLATAH AKVRLSKT V NKVDAKVAAN LLRFALLGED IGNDIDEEES EYEEALSKRS PQKSPKKRQR VRQPASNSGS PIKSTPRRST ASSVNATPS SARRILRFQD DEQNAGEDDN DIMSPLPADE EAELQRRLQL GLRVSPRRRE HLHAPEEGSS GPLTEVGTPR LPNVSSAGQD DEQQQSVIS FDNVEPGTIS TGRLSLISGI IARLMQTEIF EEESYPVASL FERINEELPE EEKFSAQEYL AGLKIMSDRN N LMVADDKV WRV

UniProtKB: DNA replication licensing factor MCM3

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Macromolecule #5: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 105.138375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSQQSSSPTK EDNNSSSPVV PNPDSVPPQL SSPALFYSSS SSQGDIYGRN NSQNLSQGEG NIRAAIGSSP LNFPSSSQRQ NSDVFQSQG RQGRIRSSAS ASGRSRYHSD LRSDRALPTS SSSLGRNGQN RVHMRRNDIH TSDLSSPRRI VDFDTRSGVN T LDTSSSSA ...String:
MSQQSSSPTK EDNNSSSPVV PNPDSVPPQL SSPALFYSSS SSQGDIYGRN NSQNLSQGEG NIRAAIGSSP LNFPSSSQRQ NSDVFQSQG RQGRIRSSAS ASGRSRYHSD LRSDRALPTS SSSLGRNGQN RVHMRRNDIH TSDLSSPRRI VDFDTRSGVN T LDTSSSSA PPSEASEPLR IIWGTNVSIQ ECTTNFRNFL MSFKYKFRKI LDEREEFINN TTDEELYYIK QLNEMRELGT SN LNLDARN LLAYKQTEDL YHQLLNYPQE VISIMDQTIK DCMVSLIVDN NLDYDLDEIE TKFYKVRPYN VGSCKGMREL NPN DIDKLI NLKGLVLRST PVIPDMKVAF FKCNVCDHTM AVEIDRGVIQ EPARCERIDC NEPNSMSLIH NRCSFADKQV IKLQ ETPDF VPDGQTPHSI SLCVYDELVD SCRAGDRIEV TGTFRSIPIR ANSRQRVLKS LYKTYVDVVH VKKVSDKRLD VDTST IEQE LMQNKVDHNE VEEVRQITDQ DLAKIREVAA REDLYSLLAR SIAPSIYELE DVKKGILLQL FGGTNKTFTK GGRYRG DIN ILLCGDPSTS KSQILQYVHK ITPRGVYTSG KGSSAVGLTA YITRDVDTKQ LVLESGALVL SDGGVCCIDE FDKMSDS TR SVLHEVMEQQ TISIAKAGII TTLNARSSIL ASANPIGSRY NPNLPVTENI DLPPPLLSRF DLVYLVLDKV DEKNDREL A KHLTNLYLED KPEHISQDDV LPVEFLTMYI SYAKEHIHPI ITEAAKTELV RAYVGMRKMG DDSRSDEKRI TATTRQLES MIRLAEAHAK MKLKNVVELE DVQEAVRLIR SAIKDYATDP KTGKIDMNLV QTGKSVIQRK LQEDLSREIM NVLKDQASDS MSFNELIKQ INEHSQDRVE SSDIQEALSR LQQEDKVIVL GEGVRRSVRL NNRV

UniProtKB: DNA replication licensing factor MCM4

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Macromolecule #6: Minichromosome maintenance protein 5

MacromoleculeName: Minichromosome maintenance protein 5 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 86.505734 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSFDRPEIYS APVLQGESPN DDDNTEIIKS FKNFILEFRL DSQFIYRDQL RNNILVKNYS LTVNMEHLIG YNEDIYKKLS DEPSDIIPL FETAITQVAK RISILSRAQS ANNNDKDPEN TSMDTDSLLL NSLPTFQLIL NSNANQIPLR DLDSEHVSKI V RLSGIIIS ...String:
MSFDRPEIYS APVLQGESPN DDDNTEIIKS FKNFILEFRL DSQFIYRDQL RNNILVKNYS LTVNMEHLIG YNEDIYKKLS DEPSDIIPL FETAITQVAK RISILSRAQS ANNNDKDPEN TSMDTDSLLL NSLPTFQLIL NSNANQIPLR DLDSEHVSKI V RLSGIIIS TSVLSSRATY LSIMCRNCRH TTSITINNFN SITGNTVSLP RSCLSTIESE SSMANESNIG DESTKKNCGP DP YIIIHES SKFIDQQFLK LQEIPELVPV GEMPRNLTMT CDRYLTNKVI PGTRVTIVGI YSIYNSKNGA GSGRSGGGNG GSG VAIRTP YIKILGIQSD VETSSIWNSV TMFTEEEEEE FLQLSRNPKL YEILTNSIAP SIFGNEDIKK AIVCLLMGGS KKIL PDGMR LRGDINVLLL GDPGTAKSQL LKFVEKVSPI AVYTSGKGSS AAGLTASVQR DPMTREFYLE GGAMVLADGG VVCID EFDK MRDEDRVAIH EAMEQQTISI AKAGITTVLN SRTSVLAAAN PIYGRYDDLK SPGDNIDFQT TILSRFDMIF IVKDDH NEE RDISIANHVI NIHTGNANAM QNQQEENGSE ISIEKMKRYI TYCRLKCAPR LSPQAAEKLS SNFVTIRKQL LINELES TE RSSIPITIRQ LEAIIRITES LAKLELSPIA QERHVDEAIR LFQASTMDAA SQDPIGGLNQ ASGTSLSEIR RFEQELKR R LPIGWSTSYQ TLRREFVDTH RFSQLALDKA LYALEKHETI QLRHQGQNIY RSGV

UniProtKB: Minichromosome maintenance protein 5

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Macromolecule #7: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 113.110211 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSPFPADTP SSNRPSNSSP PPSSIGAGFG SSSGLDSQIG SRLHFPSSSQ PHVSNSQTGP FVNDSTQFSS QRLQTDGSAT NDMEGNEPA RSFKSRALNH VKKVDDVTGE KVREAFEQFL EDFSVQSTDT GEVEKVYRAQ IEFMKIYDLN TIYIDYQHLS M RENGALAM ...String:
MSSPFPADTP SSNRPSNSSP PPSSIGAGFG SSSGLDSQIG SRLHFPSSSQ PHVSNSQTGP FVNDSTQFSS QRLQTDGSAT NDMEGNEPA RSFKSRALNH VKKVDDVTGE KVREAFEQFL EDFSVQSTDT GEVEKVYRAQ IEFMKIYDLN TIYIDYQHLS M RENGALAM AISEQYYRFL PFLQKGLRRV VRKYAPELLN TSDSLKRSEG DEGQADEDEQ QDDDMNGSSL PRDSGSSAAP GN GTSAMAT RSITTSTSPE QTERVFQISF FNLPTVHRIR DIRSEKIGSL LSISGTVTRT SEVRPELYKA SFTCDMCRAI VDN VEQSFK YTEPTFCPNP SCENRAFWTL NVTRSRFLDW QKVRIQENAN EIPTGSMPRT LDVILRGDSV ERAKPGDRCK FTGV EIVVP DVTQLGLPGV KPSSTLDTRG ISKTTEGLNS GVTGLRSLGV RDLTYKISFL ACHVISIGSN IGASSPDANS NNRET ELQM AANLQANNVY QDNERDQEVF LNSLSSDEIN ELKEMVKDEH IYDKLVRSIA PAVFGHEAVK KGILLQMLGG VHKSTV EGI KLRGDINICV VGDPSTSKSQ FLKYVVGFAP RSVYTSGKAS SAAGLTAAVV RDEEGGDYTI EAGALMLADN GICCIDE FD KMDISDQVAI HEAMEQQTIS IAKAGIHATL NARTSILAAA NPVGGRYNRK LSLRGNLNMT APIMSRFDLF FVILDDCN E KIDTELASHI VDLHMKRDEA IEPPFSAEQL RRYIKYARTF KPILTKEARS YLVEKYKELR KDDAQGFSRS SYRITVRQL ESMIRLSEAI ARANCVDEIT PSFIAEAYDL LRQSIIRVDV DDVEMDEEFD NIESQSHAAS GNNDDNDDGT GSGVITSEPP ADIEEGQSE ATARPGTSEK KKTTVTYDKY VSMMNMIVRK IAEVDREGAE ELTAVDIVDW YLLQKENDLG SLAEYWEERR L AFKVIKRL VKDRILMEIH GTRHNLRDLE NEENENNKTV YVIHPNCEVL DQLEPQDSS

UniProtKB: DNA replication licensing factor MCM6

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Macromolecule #8: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 95.049875 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSAALPSIQL PVDYNNLFNE ITDFLVTFKQ DTLSSDATRN ENEDENLDAE NIEQHLLEKG PKYMAMLQKV ANRELNSVII DLDDILQYQ NEKFLQGTQA DDLVSAIQQN ANHFTELFCR AIDNNMPLPT KEIDYKDDVL DVILNQRRLR NERMLSDRTN E IRSENLMD ...String:
MSAALPSIQL PVDYNNLFNE ITDFLVTFKQ DTLSSDATRN ENEDENLDAE NIEQHLLEKG PKYMAMLQKV ANRELNSVII DLDDILQYQ NEKFLQGTQA DDLVSAIQQN ANHFTELFCR AIDNNMPLPT KEIDYKDDVL DVILNQRRLR NERMLSDRTN E IRSENLMD TTMDPPSSMN DALREVVEDE TELFPPNLTR RYFLYFKPLS QNCARRYRKK AISSKPLSVR QIKGDFLGQL IT VRGIITR VSDVKPAVEV IAYTCDQCGY EVFQEVNSRT FTPLSECTSE ECSQNQTKGQ LFMSTRASKF SAFQECKIQE LSQ QVPVGH IPRSLNIHVN GTLVRSLSPG DIVDVTGIFL PAPYTGFKAL KAGLLTETYL EAQFVRQHKK KFASFSLTSD VEER VMELI TSGDVYNRLA KSIAPEIYGN LDVKKALLLL LVGGVDKRVG DGMKIRGDIN VCLMGDPGVA KSQLLKAICK ISPRG VYTT GKGSSGVGLT AAVMKDPVTD EMILEGGALV LADNGICCID EFDKMDESDR TAIHEVMEQQ TISISKAGIN TTLNAR TSI LAAANPLYGR YNPRLSPLDN INLPAALLSR FDILFLMLDI PSRDDDEKLA EHVTYVHMHN KQPDLDFTPV EPSKMRE YI AYAKTKRPVM SEAVNDYVVQ AYIRLRQDSK REMDSKFSFG QATPRTLLGI IRLSQALAKL RLADMVDIDD VEEALRLV R VSKESLYQET NKSKEDESPT TKIFTIIKKM LQETGKNTLS YENIVKTVRL RGFTMLQLSN CIQEYSYLNV WHLINEGNT LKFVDDGTMD TDQEDSLVST PKLAPQTTAS ANVSAQDSDI DLQDA

UniProtKB: DNA replication licensing factor MCM7

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Macromolecule #9: DNA replication regulator SLD3

MacromoleculeName: DNA replication regulator SLD3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 77.428633 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: METWEVIASV KEATKGLDLS LDHPLIIKSE DVPSNILQLL QQKNRRQLKH ICMKSRKEYF LLEEYGPGFW VKWPYNYFNG YSLPERRTE VVTTVERERA KRETLKTWDE LKFKELLHLW SEEPKGSCKL EKDKDLKLDM NPPDMKGESK INDYYSDPKE Y IESKYYDA ...String:
METWEVIASV KEATKGLDLS LDHPLIIKSE DVPSNILQLL QQKNRRQLKH ICMKSRKEYF LLEEYGPGFW VKWPYNYFNG YSLPERRTE VVTTVERERA KRETLKTWDE LKFKELLHLW SEEPKGSCKL EKDKDLKLDM NPPDMKGESK INDYYSDPKE Y IESKYYDA LFSIHTPLAY FVKSNLVRLK NTCRTKYGSD SYKIAYQAML QKFLLSIVQF KDRHDNRLLL EPFSSPIADE KR KNCLTKF VIQDENKNSS TIADLCVVLK SREIKLQILL LLEIIGLNDL DWNFRDFEKK YKLKLKKRSL NLTKKGLVRR RSK KKTSEK DKGIERITTS LDYCEQLDLY LDRACILDIL LSSETPNPDA IEASNGTIQE HKKNILDKSK EASLVGFINY VLIP YFNKK VPHAVEFIIQ KLKGPSMRPK RALKKVNDST NVSSPNTVET YNRLSTSQRA SRSSIINSVP SSPALRRVDA NLFSR KSIA SPTPELLNSR TNSNLNEFLE SETRSLKRPS QLGRTKSDLT MNHLQKRQFS VSDLSTTRVP NSSTITLKTP FSHSTI NAY KTMNNSFRRV GKRKDINETI RLHERVDSEE NVQVQATPAV KKRTVTPNKK AQLQSIIESP LNFKDDDTHE GRKNTSN IT STPTNKPPEN SSKRRVRRRL FAPEST

UniProtKB: DNA replication regulator SLD3

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Macromolecule #10: Cell division control protein 45

MacromoleculeName: Cell division control protein 45 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 74.324836 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MYYGISQFSE AYNKILRNSS SHSSCQLVIF VSCLNIDALC ATKMLSLLFK KQLVQSQIVP IFGYSELRRH YSQLDDNINS LLLVGFGGV IDLEAFLEID PQEYVIDTDE KSGEQSFRRD IYVLDAHRPW NLDNIFGSQI IQCFDDGTVD DTLGEQKEAY Y KLLELDEE ...String:
MYYGISQFSE AYNKILRNSS SHSSCQLVIF VSCLNIDALC ATKMLSLLFK KQLVQSQIVP IFGYSELRRH YSQLDDNINS LLLVGFGGV IDLEAFLEID PQEYVIDTDE KSGEQSFRRD IYVLDAHRPW NLDNIFGSQI IQCFDDGTVD DTLGEQKEAY Y KLLELDEE SGDDELSGDE NDNNGGDDEA TDADEVTDED EEDEDETISN KRGNSSIGPN DLSKRKQRKK QIHEYEGVLE EY YSQGTTV VNSISAQIYS LLSAIGETNL SNLWLNILGT TSLDIAYAQV YNRLYPLLQD EVKRLTPSSR NSVKTPDTLT LNI QPDYYL FLLRHSSLYD SFYYSNYVNA KLSLWNENGK KRLHKMFARM GIPLSTAQET WLYMDHSIKR ELGIIFDKNL DRYG LQDII RDGFVRTLGY RGSISASEFV EALTALLEVG NSTDKDSVKI NNDNNDDTDG EEEEDNSAQK LTNLRKRWVS NFWLS WDAL DDRKVELLNR GIQLAQDLQR AIFNTGVAIL EKKLIKHLRI YRLCVLQDGP DLDLYRNPLT LLRLGNWLIE CCAESE DKQ LLPMVLASID ENTDTYLVAG LTPRYPRGLD TIHTKKPILN NFSMAFQQIT AETDAKVRID NFESSIIEIR REDLSPF LE KLTLSGLL

UniProtKB: Cell division control protein 45

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Macromolecule #11: Mitochondrial morphogenesis protein SLD7

MacromoleculeName: Mitochondrial morphogenesis protein SLD7 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.598828 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSRKLCTLNF TLSGKQGSLV IRDIQLWSNR PTASKSTSEL RGQFIQYVDL AKLPLWVRST NMNTYRCYST SATAQAYFKS KLRNANRGI VIELFDKVDQ RSQEPAYLII FRENTELNCF QVDLTMKHEF DGQVTKLKQD IGKTRASVSK EGSIDIIIQQ S QQRKIGTK ...String:
MSRKLCTLNF TLSGKQGSLV IRDIQLWSNR PTASKSTSEL RGQFIQYVDL AKLPLWVRST NMNTYRCYST SATAQAYFKS KLRNANRGI VIELFDKVDQ RSQEPAYLII FRENTELNCF QVDLTMKHEF DGQVTKLKQD IGKTRASVSK EGSIDIIIQQ S QQRKIGTK TEVYRNVHIN DKRLQFNETL SKLILGGLRL RGISNSITDY QKLYKITFDA AEFTHRDELK RISMGSGEEV SF ESLQETV ETLLKLFTKS

UniProtKB: Mitochondrial morphogenesis protein SLD7

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Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.1 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time: 30 s Blotting time: 1.5 s Blot force: +2.

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: INTEGRATING / #0 - Number grids imaged: 1 / #0 - Number real images: 10192 / #0 - Average electron dose: 58.4 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Detector mode: INTEGRATING / #1 - Number grids imaged: 1 / #1 - Number real images: 6046 / #1 - Average electron dose: 62.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARC (ver. 4.6.2)
RELION (ver. 4.0)post-process
PHENIX (ver. 1.21.2-5419)phenix.combine_focused_maps

Details: 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 ...Details: 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)
Number images used: 292336
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)

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Atomic model buiding 1

Initial model
PDB IDChain

7pt6

source_name: PDB, initial_model_type: experimental model

7p30

source_name: PDB, initial_model_type: experimental model

5bk4

source_name: PDB, initial_model_type: experimental model

3wi3

source_name: PDB, initial_model_type: experimental model

3x38

source_name: PDB, initial_model_type: experimental model

6u0m

source_name: PDB, initial_model_type: experimental model
Output model

PDB-9th8:
Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

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