› 6ldm

X-ray diffraction
2.4Å resolution

Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1

Released:
DOI: 10.2210/pdb6ldm/pdb
PDB entry 6ldm coloured by chain, front view.
PDB entry 6ldm coloured by chain, side view.
PDB entry 6ldm coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1.
Traczyk A, Liew CW, Gill DJ, Rhodes D
Nucleic Acids Res 48 4562-4571 (2020)
PMID: 32187364

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120215 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA-binding protein RAP1 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P11938 (Residues: 353-598; Coverage: 30%)
Gene names: GRF1, N1310, RAP1, TUF1, YNL216W
Sequence domains:
G-guadruplex DNA Chain: B
Molecule details ›
Chain: B
Length: 19 nucleotides
Theoretical weight: 6.03 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand GOL 1 x GOL
Ligand TRS 1 x TRS
Ligand NA 11 x NA
Ligand K 5 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 84.68Å b: 70.2Å c: 64.85Å
α: 90° β: 97.72° γ: 90°
R-values:
R R work R free
0.204 0.203 0.233
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

The Simple Biology of Flipons and Condensates Enhances the Evolution of Complexity.
Herbert A. (2021)
1 more

3 mentions without citation

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy.
Cheng et al. (2021)
2 more