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- EMDB-53973: Phospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-53973
TitlePhospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA
Map dataLocal Refinement of DH-37-45 cryoSPARC Unsharpened map
Sample
  • Complex: Phospho-DH bound by Sld3/7 and Cdc45 on replication origin
    • Protein or peptide: x 9 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsMacromolecular Complex / DNA / ATPase / Helicase / MCM2-7 / 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 / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / 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 / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / mitotic DNA replication / nuclear pre-replicative complex / CMG complex / DNA replication preinitiation complex / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / MCM complex / mitotic DNA replication initiation / silent mating-type cassette heterochromatin formation / single-stranded DNA helicase activity / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / nuclear replication fork / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / subtelomeric heterochromatin formation / DNA helicase activity / helicase activity / transcription elongation by RNA polymerase II / spindle pole / peroxisome / nuclear envelope / heterochromatin formation / single-stranded DNA binding / DNA helicase / chromosome, telomeric region / DNA replication / DNA damage response / chromatin binding / chromatin / endoplasmic reticulum / ATP hydrolysis activity / zinc ion binding / 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 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / 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 (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPuehringer T / Couves EC / Costa A
Funding support United Kingdom, European Union, Germany, 4 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001065 United Kingdom
The Francis Crick InstituteFC001066 United Kingdom
European Research Council (ERC)820102European Union
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: Structure of the pre-initiation complex explains CMG biogenesis
Authors: Puehringer T / Canal B / Palm G / Butryn A / Couves EC / Willhoft O / Lewis JS / Diffley JFX / Costa A
History
DepositionJun 9, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53973.png

Downloads & links

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Map

FileDownload / File: emd_53973.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal Refinement of DH-37-45 cryoSPARC Unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.3025601 - 0.7824749
Average (Standard dev.)0.0023293062 (±0.024115937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local Refinement of DH-37-45 cryoSPARC subtraction Unsharpened map

Fileemd_53973_additional_1.map
AnnotationLocal Refinement of DH-37-45 cryoSPARC subtraction Unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local Refinement of DH-37-45 cryoSPARC subtraction Density-modified (DeepEMhancer)...

Fileemd_53973_additional_2.map
AnnotationLocal Refinement of DH-37-45 cryoSPARC subtraction Density-modified (DeepEMhancer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local Refinement of DH-37-45 cryoSPARC Density-modified (EMReady)

Fileemd_53973_additional_3.map
AnnotationLocal Refinement of DH-37-45 cryoSPARC Density-modified (EMReady)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local Refinement of DH-37-45 cryoSPARC Half map 1

Fileemd_53973_half_map_1.map
AnnotationLocal Refinement of DH-37-45 cryoSPARC Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local Refinement of DH-37-45 cryoSPARC Half map 2

Fileemd_53973_half_map_2.map
AnnotationLocal Refinement of DH-37-45 cryoSPARC Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phospho-DH bound by Sld3/7 and Cdc45 on replication origin

EntireName: Phospho-DH bound by Sld3/7 and Cdc45 on replication origin
Components
  • Complex: Phospho-DH bound by Sld3/7 and Cdc45 on replication origin
    • Protein or peptide: Mitochondrial morphogenesis protein SLD7
    • Protein or peptide: DNA replication regulator SLD3
    • DNA: DNA (53-MER)
    • DNA: DNA (53-MER)
    • Protein or peptide: Cell division control protein 45
    • 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
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Phospho-DH bound by Sld3/7 and Cdc45 on replication origin

SupramoleculeName: Phospho-DH bound by Sld3/7 and Cdc45 on replication origin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Mitochondrial morphogenesis protein SLD7

MacromoleculeName: Mitochondrial morphogenesis protein SLD7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.598828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #2: DNA replication regulator SLD3

MacromoleculeName: DNA replication regulator SLD3 / type: protein_or_peptide / ID: 2
Details: S. cerevisiae SLD3 in frame with C-terminal TEV protease cleavage site and Twin-Strep-Tag
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 81.240672 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 FAPESTENLY FQGWSHPQFE KGGGSGGGSG GSSAWSHPQF EK

UniProtKB: DNA replication regulator SLD3

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Macromolecule #5: Cell division control protein 45

MacromoleculeName: Cell division control protein 45 / type: protein_or_peptide / ID: 5
Details: Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 75.154703 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 YKDDDGDYKD DDETISNKRG NSSIGPNDLS KRKQRKKQIH EY EGVLEEY YSQGTTVVNS ISAQIYSLLS AIGETNLSNL WLNILGTTSL DIAYAQVYNR LYPLLQDEVK RLTPSSRNSV KTP DTLTLN IQPDYYLFLL RHSSLYDSFY YSNYVNAKLS LWNENGKKRL HKMFARMGIP LSTAQETWLY MDHSIKRELG IIFD KNLDR YGLQDIIRDG FVRTLGYRGS ISASEFVEAL TALLEVGNST DKDSVKINND NNDDTDGEEE EDNSAQKLTN LRKRW VSNF WLSWDALDDR KVELLNRGIQ LAQDLQRAIF NTGVAILEKK LIKHLRIYRL CVLQDGPDLD LYRNPLTLLR LGNWLI ECC AESEDKQLLP MVLASIDENT DTYLVAGLTP RYPRGLDTIH TKKPILNNFS MAFQQITAET DAKVRIDNFE SSIIEIR RE DLSPFLEKLT LSGLL

UniProtKB: Cell division control protein 45, Cell division control protein 45

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Macromolecule #6: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / 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: 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 #7: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 7
Details: N-terminal CBP tag followed by TEV protease cleavage site in frame with MCM3
Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 111.720242 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKRRWKKNFI AVSAANRFKK ISSSGALENL YFQGEMEGST GFDGDATTFF APDAVFGDRV RRFQEFLDTF TSYRDSVRSI QVYNSNNAA NYNDDQDDAD ERDLLGDDDG DDLEKEKKAA SSTSLNILPH RIIISLDDLR EFDRSFWSGI LVEPAYFIPP A EKALTDLA ...String:
MKRRWKKNFI AVSAANRFKK ISSSGALENL YFQGEMEGST GFDGDATTFF APDAVFGDRV RRFQEFLDTF TSYRDSVRSI QVYNSNNAA NYNDDQDDAD ERDLLGDDDG DDLEKEKKAA SSTSLNILPH RIIISLDDLR EFDRSFWSGI LVEPAYFIPP A EKALTDLA DSMDDVPHPN ASAVSSRHPW KLSFKGSFGA HALSPRTLTA QHLNKLVSVE GIVTKTSLVR PKLIRSVHYA AK TGRFHYR DYTDATTTLT TRIPTPAIYP TEDTEGNKLT TEYGYSTFID HQRITVQEMP EMAPAGQLPR SIDVILDDDL VDK TKPGDR VNVVGVFKSL GAGGMNQSNS NTLIGFKTLI LGNTVYPLHA RSTGVAARQM LTDFDIRNIN KLSKKKDIFD ILSQ SLAPS IYGHDHIKKA ILLMLMGGVE KNLENGSHLR GDINILMVGD PSTAKSQLLR FVLNTASLAI ATTGRGSSGV GLTAA VTTD RETGERRLEA GAMVLADRGV VCIDEFDKMT DVDRVAIHEV MEQQTVTIAK AGIHTTLNAR CSVIAAANPV FGQYDV NRD PHQNIALPDS LLSRFDLLFV VTDDINEIRD RSISEHVLRT HRYLPPGYLE GEPVRERLNL SLAVGEDADI NPEEHSN SG AGVENEGEDD EDHVFEKFNP LLQAGAKLAK NKGNYNGTEI PKLVTIPFLR KYVQYAKERV IPQLTQEAIN VIVKNYTD L RNDDNTKKSP ITARTLETLI RLATAHAKVR LSKTVNKVDA KVAANLLRFA LLGEDIGNDI DEEESEYEEA LSKRSPQKS PKKRQRVRQP ASNSGSPIKS TPRRSTASSV NATPSSARRI LRFQDDEQNA GEDDNDIMSP LPADEEAELQ RRLQLGLRVS PRRREHLHA PEEGSSGPLT EVGTPRLPNV SSAGQDDEQQ QSVISFDNVE PGTISTGRLS LISGIIARLM QTEIFEEESY P VASLFERI NEELPEEEKF SAQEYLAGLK IMSDRNNLMV ADDKVWRV

UniProtKB: DNA replication licensing factor MCM3

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Macromolecule #8: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / 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: 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 #9: Minichromosome maintenance protein 5

MacromoleculeName: Minichromosome maintenance protein 5 / type: protein_or_peptide / ID: 9 / 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 #10: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 10 / 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 #11: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 11 / 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 #3: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.326441 KDa
SequenceString: (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)(DT) (DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC) (DA) (DT)(DG)(DC)(DG)(DC)(DA) ...String:
(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)(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)

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Macromolecule #4: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.335457 KDa
SequenceString: (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)(DG)(DC)(DA)(DT) (DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC) (DA) (DT)(DG)(DC)(DG)(DC)(DA) ...String:
(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)(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)

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 4 / 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 #14: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 105652 / Average electron dose: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 5610789
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab initio volume
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72693
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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