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Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding Domains Bound to a DR3 Response Element

X-ray diffraction
3Å resolution
PDB entry 1ynw coloured by chain, front view.
PDB entry 1ynw coloured by chain, side view.
PDB entry 1ynw coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: RXRalpha-VDR nuclear hormone receptor complex and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 15449.09 Å2
Buried surface area: 4736.0 Å2
Dissociation area: 732.92 Å2
Dissociation energy (ΔGdiss): 3.99 kcal/mol
Dissociation entropy (TΔSdiss): 10.95 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-114864

Macromolecules

Vitamin D3 receptor
Chain: A
Length: 110 amino acids
Theoretical weight: 12.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11473 (Residues: 16-125; Coverage: 26%)
Gene names: NR1I1, VDR
Pfam: Zinc finger, C4 type (two domains)
InterPro:
CATH: Erythroid Transcription Factor GATA-1, subunit A
SCOP: Nuclear receptor
Vitamin D3 receptor in PDB entry 1ynw, assembly 1, front view.
Vitamin D3 receptor in PDB entry 1ynw, assembly 1, side view.
Vitamin D3 receptor in PDB entry 1ynw, assembly 1, top view.
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Retinoic acid receptor RXR-alpha
Chain: B
Length: 99 amino acids
Theoretical weight: 11.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19793 (Residues: 130-228; Coverage: 21%)
Gene names: NR2B1, RXRA
Pfam: Zinc finger, C4 type (two domains)
InterPro:
CATH: Erythroid Transcription Factor GATA-1, subunit A
SCOP: Nuclear receptor
Retinoic acid receptor RXR-alpha in PDB entry 1ynw, assembly 1, front view.
Retinoic acid receptor RXR-alpha in PDB entry 1ynw, assembly 1, side view.
Retinoic acid receptor RXR-alpha in PDB entry 1ynw, assembly 1, top view.
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DNA chain C
Name: 5'-d(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A)-3'
Representative chains: C
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
5'-d(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A)-3' in PDB entry 1ynw, assembly 1, front view.
5'-d(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A)-3' in PDB entry 1ynw, assembly 1, side view.
5'-d(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A)-3' in PDB entry 1ynw, assembly 1, top view.
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DNA chain D
Name: 5'-d(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A)-3'
Representative chains: D
Length: 18 nucleotides
Theoretical weight: 5.46 KDa
5'-d(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A)-3' in PDB entry 1ynw, assembly 1, front view.
5'-d(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A)-3' in PDB entry 1ynw, assembly 1, side view.
5'-d(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A)-3' in PDB entry 1ynw, assembly 1, top view.
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