7PT6

Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer.

Saleh, A.Noguchi, Y.Aramayo, R.Ivanova, M.E.Stevens, K.M.Montoya, A.Sunidhi, S.Carranza, N.L.Skwark, M.J.Speck, C.

(2022) Nat Commun 13: 2915-2915

  • DOI: https://doi.org/10.1038/s41467-022-30576-1
  • Primary Citation of Related Structures:  
    7PT6, 7PT7

  • PubMed Abstract: 

    The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. Using cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6. In summary, our work provides fundamental insights into DDK structure, control and selective activation of the MCM2-7 helicase during DNA replication. Importantly, these insights can be exploited for development of novel DDK inhibitors.


  • Organizational Affiliation

    DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Undefined Mcm4 flexible N-terminal tailA [auth 1],
J [auth A]
4Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2B [auth 2],
K [auth B]
868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29469 
Go to UniProtKB:  P29469
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29469
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3C [auth 3],
L [auth C]
971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P24279 
Go to UniProtKB:  P24279
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24279
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4D [auth 4],
M [auth D]
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))
Explore P30665 
Go to UniProtKB:  P30665
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30665
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5E [auth 5],
N [auth E]
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))
Explore P29496 
Go to UniProtKB:  P29496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29496
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6F [auth 6],
O [auth F]
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))
Explore P53091 
Go to UniProtKB:  P53091
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53091
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7G [auth 7],
P [auth G]
845Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38132 
Go to UniProtKB:  P38132
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38132
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 7H [auth 8],
Q [auth H]
507Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC7OAF2YDL017WD2855
EC: 2.7.11.1
UniProt
Find proteins for P06243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06243 
Go to UniProtKB:  P06243
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06243
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DDK kinase regulatory subunit DBF4I [auth 9],
R [auth I]
704Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DBF4DNA52YDR052CD4205YD9609.07C
UniProt
Find proteins for P32325 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32325 
Go to UniProtKB:  P32325
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32325
Sequence Annotations
Expand
  • 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 5]
CA [auth 6]
DA [auth 6]
GB [auth H]
KA [auth 8]
AA [auth 5],
CA [auth 6],
DA [auth 6],
GB [auth H],
KA [auth 8],
OA [auth B],
S [auth 2],
UA [auth D],
WA [auth E],
Y [auth 4],
YA [auth F],
ZA [auth F]
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 
DB [auth G],
HA [auth 7],
SA [auth C],
W [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 5]
BB [auth F]
FA [auth 6]
FB [auth G]
IB [auth H]
BA [auth 5],
BB [auth F],
FA [auth 6],
FB [auth G],
IB [auth H],
JA [auth 7],
JB [auth I],
MA [auth 8],
NA [auth 9],
QA [auth B],
U [auth 2],
VA [auth D],
XA [auth E],
Z [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth F]
CB [auth G]
EA [auth 6]
EB [auth G]
GA [auth 7]
AB [auth F],
CB [auth G],
EA [auth 6],
EB [auth G],
GA [auth 7],
HB [auth H],
IA [auth 7],
LA [auth 8],
PA [auth B],
RA [auth B],
T [auth 2],
TA [auth C],
V [auth 2],
X [auth 3]
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
RECONSTRUCTIONRELION
RECONSTRUCTIONPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T005378/1
Wellcome TrustUnited Kingdom107903/Z/15/Z
Medical Research Council (MRC, United Kingdom)United KingdomA652-5PY40
Wellcome TrustUnited Kingdom206175/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release