7V3U | pdb_00007v3u

Cryo-EM structure of MCM double hexamer with structured Mcm4-NSD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7V3U

This is version 1.2 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 1,219.77 kDa 
  • Atom Count: 62,646 
  • Modeled Residue Count: 7,898 
  • Deposited Residue Count: 10,818 
  • Unique protein chains: 6

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
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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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
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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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
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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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
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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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
UniProt
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Reference Sequence
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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
UniProt
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
(Subject of Investigation/LOI)

Query on AGS



Download:Ideal Coordinates CCD File
AA [auth 7]
DA [auth B]
IA [auth D]
LA [auth E]
M [auth 2]
AA [auth 7],
DA [auth B],
IA [auth D],
LA [auth E],
M [auth 2],
OA [auth F],
R [auth 4],
RA [auth G],
U [auth 5],
X [auth 6]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
GA [auth C],
P [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
CA [auth 7]
FA [auth B]
KA [auth D]
NA [auth E]
O [auth 2]
CA [auth 7],
FA [auth B],
KA [auth D],
NA [auth E],
O [auth 2],
QA [auth F],
T [auth 4],
TA [auth G],
W [auth 5],
Z [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
BA [auth 7]
EA [auth B]
HA [auth C]
JA [auth D]
MA [auth E]
BA [auth 7],
EA [auth B],
HA [auth C],
JA [auth D],
MA [auth E],
N [auth 2],
PA [auth F],
Q [auth 3],
S [auth 4],
SA [auth G],
V [auth 5],
Y [auth 6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection