› 8p62

Electron Microscopy
3.9Å resolution

S. cerevisiae ssDNA-sCMGE after DNA replication initiation

Released:
DOI: 10.2210/pdb8p62/pdb
PDB entry 8p62 coloured by chain, front view.
PDB entry 8p62 coloured by chain, side view.
PDB entry 8p62 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Unwinding of a eukaryotic origin of replication visualized by cryo-EM.
Henrikus SS, Gross MH, Willhoft O, Pühringer T, Lewis JS, McClure AW, Greiwe JF, Palm G, Nans A, Diffley JFX, Costa A
Nat Struct Mol Biol (2024)
PMID: 38760633
Related structures: EMD-17458

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270633 (preferred)
Entry contents:
13 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (14 distinct):
DNA replication licensing factor MCM2 Chain: 2
Molecule details ›
Chain: 2
Length: 868 amino acids
Theoretical weight: 98.91 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P29469 (Residues: 1-868; Coverage: 100%)
Gene names: MCM2, YBL023C, YBL0438
Sequence domains:
DNA replication licensing factor MCM3 Chain: 3
Molecule details ›
Chain: 3
Length: 1006 amino acids
Theoretical weight: 111.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P24279 (Residues: 1-971; Coverage: 100%)
Gene names: MCM3, SYGP-ORF23, YEL032W
Sequence domains:
DNA replication licensing factor MCM4 Chain: 4
Molecule details ›
Chain: 4
Length: 933 amino acids
Theoretical weight: 105.14 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30665 (Residues: 1-933; Coverage: 100%)
Gene names: CDC54, HCD21, MCM4, YP9531.13, YPR019W
Sequence domains:
Minichromosome maintenance protein 5 Chain: 5
Molecule details ›
Chain: 5
Length: 775 amino acids
Theoretical weight: 86.51 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P29496 (Residues: 1-775; Coverage: 100%)
Gene names: CDC46, L9328.1, MCM5, YLR274W
Sequence domains:
DNA replication licensing factor MCM6 Chain: 6
Molecule details ›
Chain: 6
Length: 1017 amino acids
Theoretical weight: 113.11 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53091 (Residues: 1-1017; Coverage: 100%)
Gene names: MCM6, YGL201C
Sequence domains:
DNA replication licensing factor MCM7 Chain: 7
Molecule details ›
Chain: 7
Length: 845 amino acids
Theoretical weight: 95.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38132 (Residues: 1-845; Coverage: 100%)
Gene names: CDC47, MCM7, YBR1441, YBR202W
Sequence domains:
DNA replication complex GINS protein PSF3 Chain: C
Molecule details ›
Chain: C
Length: 229 amino acids
Theoretical weight: 25.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12146 (Residues: 1-194; Coverage: 100%)
Gene names: PSF3, YOL146W
Sequence domains:
DNA replication complex GINS protein SLD5 Chain: D
Molecule details ›
Chain: D
Length: 294 amino acids
Theoretical weight: 33.98 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03406 (Residues: 1-294; Coverage: 100%)
Gene names: SLD5, YDR489W
Sequence domains:
Cell division control protein 45 Chain: E
Molecule details ›
Chain: E
Length: 657 amino acids
Theoretical weight: 75.15 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08032 (Residues: 1-203, 204-650; Coverage: 100%)
Gene names: CDC45, L8004.11, SLD4, YLR103C
Sequence domains: CDC45-like protein
DNA polymerase epsilon subunit B Chain: F
Molecule details ›
Chain: F
Length: 689 amino acids
Theoretical weight: 78.43 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P24482 (Residues: 1-689; Coverage: 100%)
Gene names: DPB2, P9705.7, YPR175W
Sequence domains: DNA polymerase alpha/epsilon subunit B
DNA polymerase epsilon catalytic subunit A Chain: G
Molecule details ›
Chain: G
Length: 2222 amino acids
Theoretical weight: 255.99 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21951 (Residues: 1-2222; Coverage: 100%)
Gene names: DUN2, N0825, POL2, YNL262W
Sequence domains:
DNA replication complex GINS protein PSF1 Chain: H
Molecule details ›
Chain: H
Length: 208 amino acids
Theoretical weight: 24.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12488 (Residues: 1-208; Coverage: 100%)
Gene names: PSF1, PZA208, YD8119.18, YDR013W
Sequence domains: GINS complex protein helical bundle domain
DNA replication complex GINS protein PSF2 Chain: I
Molecule details ›
Chain: I
Length: 213 amino acids
Theoretical weight: 25.1 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P40359 (Residues: 1-213; Coverage: 100%)
Gene names: HRF213, J1086, PSF2, YJL072C
Sequence domains: GINS complex protein helical bundle domain
DNA (9-MER) Chain: A
Molecule details ›
Chain: A
Length: 9 nucleotides
Theoretical weight: 2.77 KDa

Ligands and Environments

4 bound ligands:
Ligand ATP 4 x ATP
Ligand ZN 7 x ZN
Ligand MG 3 x MG
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-17458
Expression systems:
  • Saccharomyces cerevisiae
  • Escherichia coli

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