› 7p5z

Electron Microscopy
3.3Å resolution

Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase

Released:
DOI: 10.2210/pdb7p5z/pdb
PDB entry 7p5z coloured by chain, front view.
PDB entry 7p5z coloured by chain, side view.
PDB entry 7p5z coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase.
Greiwe JF, Miller TCR, Locke J, Martino F, Howell S, Schreiber A, Nans A, Diffley JFX, Costa A
OpenAccess logo Nat Struct Mol Biol 29 10-20 (2022)
PMID: 34963704
Related structures: EMD-13211

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-121774 (preferred)
Entry contents:
8 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (10 distinct):
DNA replication licensing factor MCM2 Chains: 2, A
Molecule details ›
Chains: 2, A
Length: 868 amino acids
Theoretical weight: 98.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P29469 (Residues: 1-868; Coverage: 100%)
Gene names: MCM2, YBL023C, YBL0438
Sequence domains:
DNA replication licensing factor MCM3 Chains: 3, B
Molecule details ›
Chains: 3, B
Length: 1006 amino acids
Theoretical weight: 111.72 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P24279 (Residues: 1-971; Coverage: 100%)
Gene names: MCM3, SYGP-ORF23, YEL032W
Sequence domains:
DNA replication licensing factor MCM4 Chains: 4, C
Molecule details ›
Chains: 4, C
Length: 933 amino acids
Theoretical weight: 105.14 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30665 (Residues: 1-933; Coverage: 100%)
Gene names: CDC54, HCD21, MCM4, YP9531.13, YPR019W
Sequence domains:
Minichromosome maintenance protein 5 Chains: 5, D
Molecule details ›
Chains: 5, D
Length: 775 amino acids
Theoretical weight: 86.51 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P29496 (Residues: 1-775; Coverage: 100%)
Gene names: CDC46, L9328.1, MCM5, YLR274W
Sequence domains:
DNA replication licensing factor MCM6 Chains: 6, E
Molecule details ›
Chains: 6, E
Length: 1017 amino acids
Theoretical weight: 113.11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53091 (Residues: 1-1017; Coverage: 100%)
Gene names: MCM6, YGL201C
Sequence domains:
DNA replication licensing factor MCM7 Chains: 7, F
Molecule details ›
Chains: 7, F
Length: 845 amino acids
Theoretical weight: 95.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38132 (Residues: 1-845; Coverage: 100%)
Gene names: CDC47, MCM7, YBR1441, YBR202W
Sequence domains:
Cell division control protein 7 Chain: 1
Molecule details ›
Chain: 1
Length: 507 amino acids
Theoretical weight: 58.39 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P06243 (Residues: 1-507; Coverage: 100%)
Gene names: CDC7, D2855, OAF2, YDL017W
Sequence domains: Protein kinase domain
DDK kinase regulatory subunit DBF4 Chain: G
Molecule details ›
Chain: G
Length: 738 amino acids
Theoretical weight: 84.5 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32325 (Residues: 1-704; Coverage: 100%)
Gene names: D4205, DBF4, DNA52, YD9609.07C, YDR052C
Sequence domains:
DNA (53-MER) Chain: X
Molecule details ›
Chain: X
Length: 53 nucleotides
Theoretical weight: 16.33 KDa
DNA (53-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 53 nucleotides
Theoretical weight: 16.34 KDa

Ligands and Environments

4 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 10 x MG
Ligand ZN 11 x ZN
Ligand ADP 8 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-13211
Expression system: Saccharomyces cerevisiae S288C

Quick links

Citations

6 review citations

The CMG helicase and cancer: a tumor "engine" and weakness with missing mutations.
Xiang et al. (2023)
5 more

1 mention without citation

Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase.
Greiwe et al. (2022)