7P30

3.0 A resolution structure of a DNA-loaded MCM double hexamer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase.

Greiwe, J.F.Miller, T.C.R.Locke, J.Martino, F.Howell, S.Schreiber, A.Nans, A.Diffley, J.F.X.Costa, A.

(2022) Nat Struct Mol Biol 29: 10-20

  • DOI: 10.1038/s41594-021-00698-z
  • Primary Citation of Related Structures:  
    7P30, 7P5Z

  • PubMed Abstract: 
  • Loading of the eukaryotic replicative helicase onto replication origins involves two MCM hexamers forming a double hexamer (DH) around duplex DNA. During S phase, helicase activation requires MCM phosphorylation by Dbf4-dependent kinase (DDK), comprising Cdc7 and Dbf4 ...

    Loading of the eukaryotic replicative helicase onto replication origins involves two MCM hexamers forming a double hexamer (DH) around duplex DNA. During S phase, helicase activation requires MCM phosphorylation by Dbf4-dependent kinase (DDK), comprising Cdc7 and Dbf4. DDK selectively phosphorylates loaded DHs, but how such fidelity is achieved is unknown. Here, we determine the cryogenic electron microscopy structure of Saccharomyces cerevisiae DDK in the act of phosphorylating a DH. DDK docks onto one MCM ring and phosphorylates the opposed ring. Truncation of the Dbf4 docking domain abrogates DH phosphorylation, yet Cdc7 kinase activity is unaffected. Late origin firing is blocked in response to DNA damage via Dbf4 phosphorylation by the Rad53 checkpoint kinase. DDK phosphorylation by Rad53 impairs DH phosphorylation by blockage of DDK binding to DHs, and also interferes with the Cdc7 active site. Our results explain the structural basis and regulation of the selective phosphorylation of DNA-loaded MCM DHs, which supports bidirectional replication.


    Organizational Affiliation

    Macromolecular Machines Laboratory, The Francis Crick Institute, London, UK. alessandro.costa@crick.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2],
G [auth A]
868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP29469
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3],
H [auth B]
1,006Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4],
I [auth C]
933Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5],
J [auth D]
775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6],
K [auth E]
1,017Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7],
L [auth F]
845Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (53-MER)M [auth X]53Saccharomyces cerevisiae S288C
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (53-MER)N [auth Y]53Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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DA [auth A],
O [auth 2]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

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AA [auth 7],
GA [auth B],
IA [auth C],
KA [auth D],
PA [auth F],
AA [auth 7],
GA [auth B],
IA [auth C],
KA [auth D],
PA [auth F],
R [auth 3],
T [auth 4],
V [auth 5]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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CA [auth 7],
FA [auth A],
JA [auth C],
MA [auth D],
NA [auth E],
CA [auth 7],
FA [auth A],
JA [auth C],
MA [auth D],
NA [auth E],
Q [auth 2],
RA [auth F],
U [auth 4],
X [auth 5],
Y [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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BA [auth 7],
EA [auth A],
HA [auth B],
LA [auth D],
OA [auth F],
BA [auth 7],
EA [auth A],
HA [auth B],
LA [auth D],
OA [auth F],
P [auth 2],
QA [auth F],
S [auth 3],
W [auth 5],
Z [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustFC001065
Medical Research Council (MRC, United Kingdom)FC001065
Cancer Research UKFC001065
European Research Council (ERC)European Union820102

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release