› 1by4

X-ray diffraction
2.1Å resolution

STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA

Released:
DOI: 10.2210/pdb1by4/pdb
PDB entry 1by4 coloured by chain, front view.
PDB entry 1by4 coloured by chain, side view.
PDB entry 1by4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of RXR-DNA interactions.
Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B, Rastinejad F
J Mol Biol 296 509-20 (2000)
PMID: 10669605

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113519 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Retinoic acid receptor RXR-alpha Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 82 amino acids
Theoretical weight: 9.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P19793 (Residues: 128-209; 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(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 16 nucleotides
Theoretical weight: 4.95 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 15 nucleotides
Theoretical weight: 4.52 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P21
Unit cell:
a: 70.93Å b: 33.65Å c: 101.4Å
α: 90° β: 89.95° γ: 90°
R-values:
R R work R free
0.234 0.234 0.284
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Overview of nomenclature of nuclear receptors.
Germain et al. (2006)
9 more

20 mentions without citation

The retinoid X receptors and their ligands.
Dawson et al. (2012)
19 more