› 8xgc

Electron Microscopy
3.7Å resolution

Structure of yeast replisome associated with FACT and histone hexamer, Composite map

Released:
DOI: 10.2210/pdb8xgc/pdb
PDB entry 8xgc coloured by chain, front view.
PDB entry 8xgc coloured by chain, side view.
PDB entry 8xgc coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Parental histone transfer caught at the replication fork.
Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, Zhou K, Liu Y, Li XD, Tye BK, Li Q, Gao N, Zhai Y
Nature 627 890-897 (2024)
PMID: 38448592
Related structures: EMD-38317

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 29-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-247604 (preferred)
Entry contents:
23 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (25 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
DNA replication licensing factor MCM3 Chain: 3
Molecule details ›
Chain: 3
Length: 971 amino acids
Theoretical weight: 107.65 KDa
Source organism: 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
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
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
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
DNA polymerase epsilon catalytic subunit A Chain: 8
Molecule details ›
Chain: 8
Length: 2222 amino acids
Theoretical weight: 255.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21951 (Residues: 1-2222; Coverage: 100%)
Gene names: DUN2, N0825, POL2, YNL262W
Sequence domains:
DNA polymerase epsilon subunit B Chain: 9
Molecule details ›
Chain: 9
Length: 689 amino acids
Theoretical weight: 78.43 KDa
Source organism: 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 replication complex GINS protein PSF1 Chain: A
Molecule details ›
Chain: A
Length: 208 amino acids
Theoretical weight: 24.23 KDa
Source organism: 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: 251 amino acids
Theoretical weight: 29.34 KDa
Source organism: Saccharomyces cerevisiae
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
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
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
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
UniProt:
  • Canonical: Q01454 (Residues: 1-927; Coverage: 100%)
Gene names: CHL15, CTF4, P9659.7, POB1, YPR135W
Sequence domains:
Topoisomerase 1-associated factor 1 Chain: I
Molecule details ›
Chain: I
Length: 1238 amino acids
Theoretical weight: 141.3 KDa
Source organism: 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: J
Molecule details ›
Chain: J
Length: 317 amino acids
Theoretical weight: 36.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04659 (Residues: 1-317; Coverage: 100%)
Gene names: CSM3, YM9796.01, YMR048W
Sequence domains: Replication Fork Protection Component Swi3
Mediator of replication checkpoint protein 1 Chain: K
Molecule details ›
Chain: K
Length: 1096 amino acids
Theoretical weight: 124.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25588 (Residues: 1-1096; Coverage: 100%)
Gene names: MRC1, YCL061C, YCL61C/YCL60C
Sequence domains: MRC1-like domain
FACT complex subunit SPT16 Chain: L
Molecule details ›
Chain: L
Length: 1035 amino acids
Theoretical weight: 118.78 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32558 (Residues: 1-1035; Coverage: 100%)
Gene names: CDC68, SPT16, SSF1, YGL207W
Sequence domains:
FACT complex subunit POB3 Chain: M
Molecule details ›
Chain: M
Length: 552 amino acids
Theoretical weight: 63.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04636 (Residues: 1-552; Coverage: 100%)
Gene names: POB3, YML069W
Sequence domains:
Histone H3 Chains: N, R
Molecule details ›
Chains: N, R
Length: 136 amino acids
Theoretical weight: 15.39 KDa
Source organism: Saccharomyces cerevisiae
Histone H4 Chains: O, S
Molecule details ›
Chains: O, S
Length: 103 amino acids
Theoretical weight: 11.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02309 (Residues: 1-103; Coverage: 100%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A.1 Chain: P
Molecule details ›
Chain: P
Length: 132 amino acids
Theoretical weight: 14.01 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04911 (Residues: 1-132; Coverage: 100%)
Gene names: H2A1, HTA1, SPT11, YD9934.10, YDR225W
Sequence domains:
Histone H2B.2 Chain: Q
Molecule details ›
Chain: Q
Length: 131 amino acids
Theoretical weight: 14.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02294 (Residues: 1-131; Coverage: 100%)
Gene names: H2B2, HTB2, YBL002W, YBL0104
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (51-MER) Chain: X
Molecule details ›
Chain: X
Length: 51 nucleotides
Theoretical weight: 15.69 KDa
DNA (39-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 39 nucleotides
Theoretical weight: 11.94 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 7 x ZN
Ligand ADP 5 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-38317

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