› 7pmn

Electron Microscopy
3.2Å resolution

S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II)

Released:
DOI: 10.2210/pdb7pmn/pdb
PDB entry 7pmn coloured by chain, front view.
PDB entry 7pmn coloured by chain, side view.
PDB entry 7pmn coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
A conserved mechanism for regulating replisome disassembly in eukaryotes.
Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD
OpenAccess logo Nature 600 743-747 (2021)
PMID: 34700328
Related structures: EMD-13539

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 22-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121821 (preferred)
Entry contents:
18 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (20 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: 1009 amino acids
Theoretical weight: 111.99 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 PSF1 Chain: A
Molecule details ›
Chain: A
Length: 208 amino acids
Theoretical weight: 24.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
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: B
Molecule details ›
Chain: B
Length: 213 amino acids
Theoretical weight: 25.1 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40359 (Residues: 1-213; Coverage: 100%)
Gene names: HRF213, J1086, PSF2, YJL072C
Sequence domains: GINS complex protein helical bundle domain
DNA replication complex GINS protein PSF3 Chain: C
Molecule details ›
Chain: C
Length: 194 amino acids
Theoretical weight: 22 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
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: Saccharomyces cerevisiae
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: 1-197, 203-650; Coverage: 99%)
Gene names: CDC45, L8004.11, SLD4, YLR103C
Sequence domains: CDC45-like protein
DNA polymerase alpha-binding protein Chains: F, G, H
Molecule details ›
Chains: F, G, H
Length: 962 amino acids
Theoretical weight: 108.61 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01454 (Residues: 1-927; Coverage: 100%)
Gene names: CHL15, CTF4, P9659.7, POB1, YPR135W
Sequence domains:
Suppressor of kinetochore protein 1 Chain: K
Molecule details ›
Chain: K
Length: 194 amino acids
Theoretical weight: 22.36 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P52286 (Residues: 1-194; Coverage: 100%)
Gene names: CBF3D, D9798.14, SKP1, YDR328C
Sequence domains:
Protein DIA2 Chain: L
Molecule details ›
Chain: L
Length: 735 amino acids
Theoretical weight: 85.37 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08496 (Residues: 1-732; Coverage: 100%)
Gene names: DIA2, YOR080W, YOR29-31
Sequence domains: F-box domain
DNA polymerase epsilon catalytic subunit A Chain: Q
Molecule details ›
Chain: Q
Length: 2222 amino acids
Theoretical weight: 255.89 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 polymerase epsilon subunit B Chain: R
Molecule details ›
Chain: R
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
Topoisomerase 1-associated factor 1 Chain: X
Molecule details ›
Chain: X
Length: 1238 amino acids
Theoretical weight: 141.3 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53840 (Residues: 1-1238; Coverage: 100%)
Gene names: N0636, TOF1, YNL273W
Sequence domains: Timeless protein
Chromosome segregation in meiosis protein 3 Chain: Y
Molecule details ›
Chain: Y
Length: 319 amino acids
Theoretical weight: 36.59 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04659 (Residues: 1-317; Coverage: 100%)
Gene names: CSM3, YM9796.01, YMR048W
Sequence domains: Replication Fork Protection Component Swi3
Leading strand template DNA Chain: I
Molecule details ›
Chain: I
Length: 115 nucleotides
Theoretical weight: 37.74 KDa
Lagging strand template DNA Chain: J
Molecule details ›
Chain: J
Length: 122 nucleotides
Theoretical weight: 35.26 KDa

Ligands and Environments

3 bound ligands:
Ligand ANP 2 x ANP
Ligand MG 2 x MG
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-13539
Expression system: Saccharomyces cerevisiae

Quick links

Citations

7 review citations

DNA replication: Mechanisms and therapeutic interventions for diseases.
Song et al. (2023)
6 more