› 8kg6

Electron Microscopy
3.07Å resolution

Yeast replisome in state I

Released:
DOI: 10.2210/pdb8kg6/pdb
PDB entry 8kg6 coloured by chain, front view.
PDB entry 8kg6 coloured by chain, side view.
PDB entry 8kg6 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Synergism between CMG helicase and leading strand DNA polymerase at replication fork.
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
OpenAccess logo Nat Commun 14 5849 (2023)
PMID: 37730685
Related structures: EMD-37211

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 icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236220 (preferred)
Entry contents:
16 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (18 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 S288C
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: 971 amino acids
Theoretical weight: 107.65 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
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 S288C
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 S288C
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 S288C
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 S288C
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 S288C
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: 21.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
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 S288C
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: 650 amino acids
Theoretical weight: 74.32 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08032 (Residues: 1-650; Coverage: 100%)
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: 927 amino acids
Theoretical weight: 104.54 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01454 (Residues: 1-927; Coverage: 100%)
Gene names: CHL15, CTF4, P9659.7, POB1, YPR135W
Sequence domains:
Topoisomerase 1-associated factor 1 Chain: K
Molecule details ›
Chain: K
Length: 1238 amino acids
Theoretical weight: 141.3 KDa
Source organism: Saccharomyces cerevisiae S288C
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: L
Molecule details ›
Chain: L
Length: 317 amino acids
Theoretical weight: 36.4 KDa
Source organism: Saccharomyces cerevisiae S288C
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
DNA polymerase epsilon catalytic subunit A Chain: M
Molecule details ›
Chain: M
Length: 2222 amino acids
Theoretical weight: 255.99 KDa
Source organism: Saccharomyces cerevisiae S288C
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: N
Molecule details ›
Chain: N
Length: 689 amino acids
Theoretical weight: 78.43 KDa
Source organism: Saccharomyces cerevisiae S288C
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 (71-mer) Chain: I
Molecule details ›
Chain: I
Length: 71 nucleotides
Theoretical weight: 22.14 KDa
DNA (61-mer) Chain: J
Molecule details ›
Chain: J
Length: 61 nucleotides
Theoretical weight: 18.52 KDa

Ligands and Environments

4 bound ligands:
Ligand ZN 7 x ZN
Ligand ADP 2 x ADP
Ligand MG 5 x MG
Ligand AGS 3 x AGS
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.07Å
Relevant EMDB volumes: EMD-37211
Expression system: Saccharomyces cerevisiae

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