› 6x6e

X-ray diffraction
2Å resolution

Glucocorticoid Receptor DNA binding domain in complex with methylated precursor for a modern recognition element (methylated pre-GBS)

Released:
DOI: 10.2210/pdb6x6e/pdb
PDB entry 6x6e coloured by chain, front view.
PDB entry 6x6e coloured by chain, side view.
PDB entry 6x6e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element.
Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA
Nucleic Acids Res 49 8923-8933 (2021)
PMID: 34289059

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120909 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Glucocorticoid receptor Chains: A, B
Molecule details ›
Chains: A, B
Length: 75 amino acids
Theoretical weight: 8.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04150 (Residues: 417-491; Coverage: 10%)
Gene names: GRL, NR3C1
Sequence domains: Zinc finger, C4 type (two domains)
DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*(5CM)P*GP*TP*TP*CP*TP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*(5CM)P*GP*TP*TP*CP*TP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.48 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 130.385Å b: 39.089Å c: 97.371Å
α: 90° β: 118.618° γ: 90°
R-values:
R R work R free
0.183 0.181 0.212
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Physicochemical models of protein-DNA binding with standard and modified base pairs.
Chiu et al. (2023)

3 mentions without citation

Structural insights into glucocorticoid receptor function.
Frank et al. (2021)
2 more