7V3V

Cryo-EM structure of MCM double hexamer bound with DDK in State I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural Insight into the MCM double hexamer activation by Dbf4-Cdc7 kinase.

Cheng, J.Li, N.Huo, Y.Dang, S.Tye, B.K.Gao, N.Zhai, Y.

(2022) Nat Commun 13: 1396-1396

  • DOI: https://doi.org/10.1038/s41467-022-29070-5
  • Primary Citation of Related Structures:  
    7V3U, 7V3V, 7W8G

  • 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 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.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2],
G [auth B]
868Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
UniProt
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UniProt GroupP29469
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3],
H [auth C]
971Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4],
I [auth D]
933Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5],
J [auth E]
775Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6],
K [auth F]
1,017Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7],
L [auth G]
845Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 7M [auth H]507Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.11.1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DDK kinase regulatory subunit DBF4N [auth I]704Saccharomyces cerevisiae S288CMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

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AA [auth 6]
CA [auth 7]
FA [auth B]
KA [auth D]
O [auth 2]
AA [auth 6],
CA [auth 7],
FA [auth B],
KA [auth D],
O [auth 2],
OA [auth E],
RA [auth F],
T [auth 4],
TA [auth G],
WA [auth H],
X [auth 5]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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IA [auth C],
R [auth 3]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth 6]
EA [auth 7]
HA [auth B]
MA [auth D]
Q [auth 2]
BA [auth 6],
EA [auth 7],
HA [auth B],
MA [auth D],
Q [auth 2],
QA [auth E],
SA [auth F],
V [auth 4],
VA [auth G],
XA [auth I],
Z [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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DA [auth 7]
GA [auth B]
JA [auth C]
LA [auth D]
NA [auth D]
DA [auth 7],
GA [auth B],
JA [auth C],
LA [auth D],
NA [auth D],
P [auth 2],
PA [auth E],
S [auth 3],
U [auth 4],
UA [auth G],
W [auth 4],
Y [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release