› 5e6c

X-ray diffraction
2.2Å resolution

Glucocorticoid receptor DNA binding domain - CCL2 NF-kB response element complex

Released:
DOI: 10.2210/pdb5e6c/pdb
PDB entry 5e6c coloured by chain, front view.
PDB entry 5e6c coloured by chain, side view.
PDB entry 5e6c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements.
Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA
Nat Commun 9 1337 (2018)
PMID: 29626214

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-118619 (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: 114 amino acids
Theoretical weight: 12.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04150 (Residues: 417-506; Coverage: 12%)
Gene names: GRL, NR3C1
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
DNA (5'-D(*AP*GP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*CP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 16 nucleotides
Theoretical weight: 4.91 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 39.083Å b: 97.407Å c: 103.852Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.233 0.271
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

Glucocorticoids in T cell development, differentiation and function.
Taves et al. (2021)
11 more

3 mentions without citation

The Biologist's Guide to the Glucocorticoid Receptor's Structure.
Deploey et al. (2023)
2 more