› 6fbr

X-ray diffraction
2.1Å resolution

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human MEp DR1 Response Element, pH 4.2

Released:
DOI: 10.2210/pdb6fbr/pdb
PDB entry 6fbr coloured by chain, front view.
PDB entry 6fbr coloured by chain, side view.
PDB entry 6fbr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Modulation of RXR-DNA complex assembly by DNA context.
Osz J, McEwen AG, Wolf J, Poussin-Courmontagne P, Peluso-Iltis C, Chebaro Y, Kieffer B, Rochel N
Mol Cell Endocrinol 481 44-52 (2019)
PMID: 30476562

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-119899 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Retinoic acid receptor RXR-alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 87 amino acids
Theoretical weight: 10.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19793 (Residues: 130-212; Coverage: 18%)
Gene names: NR2B1, RXRA
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
DNA (5'-D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.2 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.21 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand PO4 1 x PO4
Ligand PGE 1 x PGE
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P3121
Unit cell:
a: 55.659Å b: 55.659Å c: 166.131Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.178 0.232
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Peptides and Peptidomimetics as Potential Antiobesity Agents: Overview of Current Status.
Kumar MS. (2019)
2 more

1 mention without citation

Site-Specific Structure at Multiple Length Scales in Kagome Quantum Spin Liquid Candidates.
Smaha et al. (2020)