› 4cn5

X-ray diffraction
2Å resolution

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Nr1d1 Response Element

Released:
DOI: 10.2210/pdb4cn5/pdb
PDB entry 4cn5 coloured by chain, front view.
PDB entry 4cn5 coloured by chain, side view.
PDB entry 4cn5 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-117296 (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
5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3' Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.28 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3' Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.13 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand CL 5 x CL
Ligand K 4 x K
Ligand NO3 1 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: C2
Unit cell:
a: 103.286Å b: 44.327Å c: 63.915Å
α: 90° β: 98.95° γ: 90°
R-values:
R R work R free
0.17 0.167 0.227
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

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

4 mentions without citation

Mg2+ ions: do they bind to nucleobase nitrogens?
Leonarski et al. (2017)
3 more