› 5omb

X-ray diffraction
1.94Å resolution

Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain

Released:
DOI: 10.2210/pdb5omb/pdb
PDB entry 5omb coloured by chain, front view.
PDB entry 5omb coloured by chain, side view.
PDB entry 5omb coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.
Deshpande I, Seeber A, Shimada K, Keusch JJ, Gut H, Gasser SM
Mol Cell 68 431-445.e5 (2017)
PMID: 29033322

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149596 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Replication factor A protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 134 amino acids
Theoretical weight: 15.62 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P22336 (Residues: 1-132; Coverage: 21%)
Gene names: BUF2, FUN3, RFA1, RPA1, YAR007C
DNA damage checkpoint protein LCD1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 111 amino acids
Theoretical weight: 12.95 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6CUV9 (Residues: 1-109; Coverage: 16%)
Gene names: KLLA0C01892g, LCD1

Ligands and Environments

2 bound ligands:
Ligand CL 3 x CL
Ligand EDO 1 x EDO
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 34.05Å b: 94.94Å c: 170.47Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.22
Expression system: Escherichia coli BL21(DE3)

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Citations

10 review citations

Structural basis of homologous recombination.
Sun et al. (2020)
9 more

3 mentions without citation

A DNA damage-induced phosphorylation circuit enhances Mec1ATR Ddc2ATRIP recruitment to Replication Protein A.
Yates et al. (2023)
2 more