› 4cn3

X-ray diffraction
2.35Å resolution

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Gde1SpA Response Element

Released:
DOI: 10.2210/pdb4cn3/pdb
PDB entry 4cn3 coloured by chain, front view.
PDB entry 4cn3 coloured by chain, side view.
PDB entry 4cn3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of natural promoter recognition by the retinoid X nuclear receptor.
Osz J, McEwen AG, Poussin-Courmontagne P, Moutier E, Birck C, Davidson I, Moras D, Rochel N
Sci Rep 5 8216 (2015)
PMID: 25645674

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-117295 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Retinoic acid receptor RXR-alpha Chains: A, B, C
Molecule details ›
Chains: A, B, C
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
Retinoic acid receptor RXR-alpha Chain: D
Molecule details ›
Chain: D
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
5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3' Chains: E, G
Molecule details ›
Chains: E, G
Length: 17 nucleotides
Theoretical weight: 5.17 KDa
5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3' Chains: F, H
Molecule details ›
Chains: F, H
Length: 17 nucleotides
Theoretical weight: 5.24 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 52.91Å b: 69.28Å c: 138.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.179 0.249
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Binding Revisited-Avidity in Cellular Function and Signaling.
Erlendsson et al. (2020)
3 more

2 mentions without citation

A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.
Salari et al. (2018)
1 more