7yhq

Electron Microscopy
3.9Å resolution

CryoEM structure of Arabidopsis ROS1 in complex with a covalent-linked reaction intermediate at 3.9 Angstroms resolution

Released:
Primary publication:
Molecular basis of the plant ROS1-mediated active DNA demethylation.
Nat Plants 9 271-279 (2023)
PMID: 36624257
Related structures: EMD-33836

Function and Biology Details

Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-122335 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA glycosylase/AP lyase ROS1; Sex-determining region Y protein Chain: A
Molecule details ›
Chain: A
Length: 757 amino acids
Theoretical weight: 86.26 KDa
Source organisms: Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q05066 (Residues: 56-130; Coverage: 37%)
  • Canonical: Q9SJQ6 (Residues: 511-1393; Coverage: 49%)
Gene names: At2g36490, DML1, F1O11.12, ROS1, SRY, TDF
Sequence domains:
DNA (40-MER) Chain: B
Molecule details ›
Chain: B
Length: 40 nucleotides
Theoretical weight: 12.35 KDa
DNA (40-MER) Chain: C
Molecule details ›
Chain: C
Length: 40 nucleotides
Theoretical weight: 12.17 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-33836
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'