› 8b9c

Electron Microscopy
4.6Å resolution

S. cerevisiae pol alpha - replisome complex

Released:
DOI: 10.2210/pdb8b9c/pdb
PDB entry 8b9c coloured by chain, front view.
PDB entry 8b9c coloured by chain, side view.
PDB entry 8b9c coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication.
Jones ML, Aria V, Baris Y, Yeeles JTP
OpenAccess logo Mol Cell (2023)
PMID: 37506699
Related structures: EMD-15924

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-224766 (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: Trichoplusia ni
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 primase large subunit Chain: A
Molecule details ›
Chain: A
Length: 528 amino acids
Theoretical weight: 62.35 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20457 (Residues: 1-528; Coverage: 100%)
Gene names: PRI2, YKL045W, YKL258
Sequence domains: Eukaryotic and archaeal DNA primase, large subunit
DNA polymerase alpha subunit B Chain: B
Molecule details ›
Chain: B
Length: 705 amino acids
Theoretical weight: 78.87 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38121 (Residues: 1-705; Coverage: 100%)
Gene names: POL12, YBL035C, YBL0414
Sequence domains:
DNA replication complex GINS protein PSF1 Chain: C
Molecule details ›
Chain: C
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: D
Molecule details ›
Chain: D
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: E
Molecule details ›
Chain: E
Length: 217 amino acids
Theoretical weight: 24.44 KDa
Source organism: Saccharomyces cerevisiae
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: F
Molecule details ›
Chain: F
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: G
Molecule details ›
Chain: G
Length: 657 amino acids
Theoretical weight: 75.15 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08032 (Residues: 1-198, 203-650; Coverage: 99%)
Gene names: CDC45, L8004.11, SLD4, YLR103C
Sequence domains: CDC45-like protein
Mediator of replication checkpoint protein 1 Chain: P
Molecule details ›
Chain: P
Length: 1109 amino acids
Theoretical weight: 126.08 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25588 (Residues: 1-1096; Coverage: 100%)
Gene names: MRC1, YCL061C, YCL61C/YCL60C
Sequence domains: MRC1-like domain
DNA primase small subunit Chain: S
Molecule details ›
Chain: S
Length: 444 amino acids
Theoretical weight: 51.83 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10363 (Residues: 1-409; Coverage: 100%)
Gene names: PRI1, YIB8C, YIR008C
Sequence domains: DNA primase small subunit
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
DNA polymerase alpha catalytic subunit A Chain: J
Molecule details ›
Chain: J
Length: 1468 amino acids
Theoretical weight: 167.03 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P13382 (Residues: 1-1468; Coverage: 100%)
Gene names: CDC17, N2181, POL1, YNL102W
Sequence domains:
Leading strand Chain: Q
Molecule details ›
Chain: Q
Length: 84 nucleotides
Theoretical weight: 26.09 KDa
Lagging strand Chain: R
Molecule details ›
Chain: R
Length: 106 nucleotides
Theoretical weight: 32.05 KDa

Ligands and Environments

3 bound ligands:
Ligand ANP 4 x ANP
Ligand MG 4 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.6Å
Relevant EMDB volumes: EMD-15924
Expression systems:
  • Trichoplusia ni
  • Saccharomyces cerevisiae

Quick links

Citations

2 review citations

Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism.
Nasheuer et al. (2024)
1 more

1 mention without citation

How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication.
Jones et al. (2023)