Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Structural Insight into the MCM double hexamer activation by Dbf4-Cdc7 kinase.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 1396, Year 2022
Publish date	Mar 16, 2022
Authors	Jiaxuan Cheng / Ningning Li / Yunjing Huo / Shangyu Dang / Bik-Kwoon Tye / Ning Gao / Yuanliang Zhai /
PubMed Abstract	The Dbf4-dependent kinase Cdc7 (DDK) regulates DNA replication initiation by phosphorylation of the MCM double hexamer (MCM-DH) to promote helicase activation. Here, we determine a series of cryo ...The Dbf4-dependent kinase Cdc7 (DDK) regulates DNA replication initiation by phosphorylation of the MCM double hexamer (MCM-DH) to promote helicase activation. Here, we determine a series of cryo electron microscopy (cryo-EM) structures of yeast DDK bound to the MCM-DH. These structures, occupied by one or two DDKs, differ primarily in the conformations of the kinase core. The interactions of DDK with the MCM-DH are mediated exclusively by subunit Dbf4 straddling across the hexamer interface on the three N-terminal domains (NTDs) of subunits Mcm2, Mcm6, and Mcm4. This arrangement brings Cdc7 close to its only essential substrate, the N-terminal serine/threonine-rich domain (NSD) of Mcm4. Dbf4 further displaces the NSD from its binding site on Mcm4-NTD, facilitating an immediate targeting of this motif by Cdc7. Moreover, the active center of Cdc7 is occupied by a unique Dbf4 inhibitory loop, which is disengaged when the kinase core assumes wobbling conformations. This study elucidates the versatility of Dbf4 in regulating the ordered multisite phosphorylation of the MCM-DH by Cdc7 kinase during helicase activation.
External links	Nat Commun / PubMed:35296675 / PubMed Central
Methods	EM (single particle)
Resolution	2.52 - 4.0 Å
Structure data	31684 7v3u EMDB-31684, PDB-7v3u: Cryo-EM structure of MCM double hexamer with structured Mcm4-NSD Method: EM (single particle) / Resolution: 3.2 Å 31685 7v3v EMDB-31685, PDB-7v3v: Cryo-EM structure of MCM double hexamer bound with DDK in State I Method: EM (single particle) / Resolution: 2.9 Å EMDB-31686: Cryo-EM map of DDK subtracted from DH-DDK complex Method: EM (single particle) / Resolution: 3.8 Å EMDB-31687: Cryo-EM map of Dbf4-NTD engaged with Mcm2-NTD-A subtracted from DH-DDK complex Method: EM (single particle) / Resolution: 4.0 Å EMDB-31688: Cryo-EM structure of MCM double hexamer bound with two DDKs (Group I) Method: EM (single particle) / Resolution: 4.0 Å EMDB-31689: Cryo-EM structure of MCM double hexamer bound with two DDKs (Group II) Method: EM (single particle) / Resolution: 3.4 Å EMDB-31690: Cryo-EM structure of MCM double hexamer bound with two DDKs (Group III) Method: EM (single particle) / Resolution: 3.4 Å EMDB-31691: Cryo-EM structure of MCM double hexamer bound with one DDK (Group IV) Method: EM (single particle) / Resolution: 3.28 Å EMDB-31692: Cryo-EM structure of MCM double hexamer bound with one DDK (Group V) Method: EM (single particle) / Resolution: 3.2 Å EMDB-31694: Cryo-EM structure of mutant MCM double hexamer (Mcm4 delta N140) bound with DDK Method: EM (single particle) / Resolution: 3.8 Å EMDB-31695: Cryo-EM structure of mutant MCM double hexamer (Mcm4 delta N174) bound with DDK Method: EM (single particle) / Resolution: 3.9 Å EMDB-31696: Cryo-EM structure of MCM double hexamer bound with DDK in State II Method: EM (single particle) / Resolution: 3.93 Å EMDB-31699: Cryo-EM structure of mutant MCM double hexamer (Mcm4 delta N140) Method: EM (single particle) / Resolution: 3.46 Å EMDB-31700: Cryo-EM structure of mutant MCM double hexamer (Mcm4 delta N174) Method: EM (single particle) / Resolution: 2.95 Å EMDB-31701: Cryo-EM structure of MCM double hexamer phosphorylated by DDK Method: EM (single particle) / Resolution: 2.72 Å 32355 7w8g EMDB-32355, PDB-7w8g: Cryo-EM structure of MCM double hexamer Method: EM (single particle) / Resolution: 2.52 Å
Chemicals	ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	saccharomyces cerevisiae s288c (yeast)
Keywords	CELL CYCLE / DNA replication initiation / Complex / Replicative helicase / Replication / Kinase