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Structure paper

TitleStructural insights into Sld3-Sld7-dependent Cdc45 loading during replication initiation.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateAug 14, 2026
AuthorsYasunori Noguchi / Almutasem Saleh / Sarah Schneider / Marina E Ivanova / Zhuo Angel Chen / Lepakshi Ranjha / Ricardo Aramayo / Silvia Tognetti / Sarah V Faull / Juri Rappsilber / Christian Speck /
PubMed AbstractRegulated 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.
External linksNat Commun / PubMed:42733061 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 18.0 Å
Structure data

55897

9tgd

EMDB-55897, PDB-9tgd:
DDK-salt stripped phosphorylated MCM2-7 DH
Method: EM (single particle) / Resolution: 3.3 Å

55904

9tgm

EMDB-55904: Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7 (composite map)
PDB-9tgm: Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7
Method: EM (single particle) / Resolution: 3.6 Å

55918

9th8

EMDB-55918: Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (composite map)
PDB-9th8: Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55972: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (consensus map, 882k particles)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-55973: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: C2 DH core)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-55974: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: Sld3 MRD1:Mcm6)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-55975: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: Sld3 MRD2:Mcm4)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55976: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: Sld7:Mcm6)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-55980: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist states consensus map, 511k particles)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-55981: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist state I)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-55982: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist state II)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-55983: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist state III)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-55985: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (consensus map, 107k particles)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-55986: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: C2 DH core)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-55987: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: Sld3 MRD1/2:Mcm4/6)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-55988: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: Sld7:Mcm6)
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-55989: Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: Sld3 STD/Cdc45:Mcm2/5)
Method: EM (single particle) / Resolution: 5.2 Å

EMDB-55990: 3DFlex map of MCM2-7 DH-Sld3/7-Cdc45
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-56009: Cryo-EM map of MCM2-7 DH bound to DNA and two copies of Sld3-Sld7 and Cdc45 (C1 symmetry)
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-56010: Cryo-EM map of MCM2-7 DH bound to DNA and two copies of Sld3-Sld7 and Cdc45 (C2 symmetry)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-56011: Negative stain-EM map of crosslinked gradient purified Sld3-Sld7
Method: EM (single particle) / Resolution: 17.0 Å

EMDB-56012: Negative stain-EM map of crosslinked gradient purified Sld3-Sld7-Cdc45
Method: EM (single particle) / Resolution: 18.0 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

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

Source
  • Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsREPLICATION / Helicase / Activation / Phosphorylation

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