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

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Basic information

Entry
Database: PDB / ID: 9th8
TitleCryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
Components
  • (DNA replication licensing factor ...) x 5
  • (dsDNA (60-MER)) x 2
  • Cell division control protein 45
  • DNA replication regulator SLD3
  • Minichromosome maintenance protein 5
  • Mitochondrial morphogenesis protein SLD7
KeywordsREPLICATION / Helicase / Activation / Phosphorylation
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 / MCM complex binding / 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 / mitotic DNA replication preinitiation complex assembly / MCM complex binding / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / CMG complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / MCM complex / mitotic DNA replication initiation / mitotic DNA replication / silent mating-type cassette heterochromatin formation / single-stranded DNA helicase activity / 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 / DNA helicase activity / helicase activity / transcription elongation by RNA polymerase II / spindle pole / nuclear envelope / peroxisome / single-stranded DNA binding / heterochromatin formation / DNA helicase / DNA replication / chromosome, telomeric region / chromatin binding / DNA damage response / chromatin / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / zinc ion binding / 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
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / 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 ...ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSaleh, A. / Noguchi, Y. / Schneider, S. / Aramayo, R. / Speck, C.
Funding support United Kingdom, 3items
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: Noguchi, Y. / Saleh, A. / Schneider, S. / Ivanova, M.E. / Chen, Z.A. / Ranjha, L. / Aramayo, R. / Tognetti, S. / Faull, S.V. / Rappsilber, J. / Speck, C.
History
DepositionDec 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: dsDNA (60-MER)
S: dsDNA (60-MER)
B: DNA replication licensing factor MCM2
C: DNA replication licensing factor MCM3
D: DNA replication licensing factor MCM4
E: Minichromosome maintenance protein 5
F: DNA replication licensing factor MCM6
G: DNA replication licensing factor MCM7
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: Minichromosome maintenance protein 5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
X: DNA replication regulator SLD3
Z: Cell division control protein 45
Y: Mitochondrial morphogenesis protein SLD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,435,14635
Polymers1,431,07417
Non-polymers4,07218
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA chain , 2 types, 2 molecules OS

#1: DNA chain dsDNA (60-MER)


Mass: 18491.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
#2: DNA chain dsDNA (60-MER)


Mass: 18491.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)

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DNA replication licensing factor ... , 5 types, 10 molecules B2C3D4F6G7

#3: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2


Mass: 98911.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM2, YBL023C, YBL0438 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29469, DNA helicase
#4: Protein DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 107653.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM3, YEL032W, SYGP-ORF23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24279, DNA helicase
#5: Protein DNA replication licensing factor MCM4 / Cell division control protein 54


Mass: 105138.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM4, CDC54, HCD21, YPR019W, YP9531.13 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30665, DNA helicase
#7: Protein DNA replication licensing factor MCM6 / Minichromosome maintenance protein 6


Mass: 113110.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM6, YGL201C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53091, DNA helicase
#8: Protein DNA replication licensing factor MCM7 / Cell division control protein 47 / Minichromosome maintenance protein 7


Mass: 95049.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM7, CDC47, YBR202W, YBR1441 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38132, DNA helicase

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Protein , 4 types, 5 molecules E5XZY

#6: Protein Minichromosome maintenance protein 5 / Cell division control protein 46


Mass: 86505.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM5, CDC46, YLR274W, L9328.1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29496, DNA helicase
#9: Protein DNA replication regulator SLD3


Mass: 77428.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLD3, YGL113W, G2980 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53135
#10: Protein Cell division control protein 45


Mass: 74324.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC45, SLD4, YLR103C, L8004.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08032
#11: Protein Mitochondrial morphogenesis protein SLD7 / Synthetic lethality with DPB11-24 mutation protein 7


Mass: 29598.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLD7, YOR060C, YOR29-11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08457

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Non-polymers , 2 types, 18 molecules

#12: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA / Type: COMPLEX / Entity ID: #1-#11 / Source: RECOMBINANT
Molecular weightValue: 1.65 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Wait time: 30 s Blotting time: 1.5 s Blot force: +2

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector modelNum. of grids imagedNum. of real images
1158.4INTEGRATINGFEI FALCON III (4k x 4k)110192
2162.1INTEGRATINGFEI FALCON III (4k x 4k)16046

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4.1.14CTF correction
9RELION4initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11cryoSPARC4.6.2classification
12cryoSPARC4.6.23D reconstruction
13RELION43D reconstructionpost-process
14PHENIX1.21.2-54193D reconstructionphenix.combine_focused_maps
15PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 292336
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)
Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17PT6

7pt6

17PT61PDBexperimental model
27P30

7p30

17P302PDBexperimental model
35BK4

5bk4

15BK43PDBexperimental model
43WI3

3wi3

13WI3PDBexperimental model
53X38

3x38

13X38PDBexperimental model
66U0M

6u0m

16U0MPDBexperimental model
RefinementHighest resolution: 2.9 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00373672
ELECTRON MICROSCOPYf_angle_d0.71100155
ELECTRON MICROSCOPYf_dihedral_angle_d12.77910994
ELECTRON MICROSCOPYf_chiral_restr0.04511588
ELECTRON MICROSCOPYf_plane_restr0.00512465

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