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

X-ray diffraction
2Å resolution
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
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: RXRalpha-RXRalpha retinoic acid receptor complex and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 12788.35 Å2
Buried surface area: 7798.22 Å2
Dissociation area: 1,153.06 Å2
Dissociation energy (ΔGdiss): 13.29 kcal/mol
Dissociation entropy (TΔSdiss): 11.3 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117296

Macromolecules

Retinoic acid receptor RXR-alpha
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
Pfam: Zinc finger, C4 type (two domains)
InterPro:
CATH: Erythroid Transcription Factor GATA-1, subunit A
Retinoic acid receptor RXR-alpha in PDB entry 4cn5, assembly 1, front view.
Retinoic acid receptor RXR-alpha in PDB entry 4cn5, assembly 1, side view.
Retinoic acid receptor RXR-alpha in PDB entry 4cn5, assembly 1, top view.
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DNA chain C
Name: 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3'
Representative chains: C
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 17 nucleotides
Theoretical weight: 5.28 KDa
5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3' in PDB entry 4cn5, assembly 1, front view.
5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3' in PDB entry 4cn5, assembly 1, side view.
5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3' in PDB entry 4cn5, assembly 1, top view.
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DNA chain D
Name: 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3'
Representative chains: D
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 17 nucleotides
Theoretical weight: 5.13 KDa
5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3' in PDB entry 4cn5, assembly 1, front view.
5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3' in PDB entry 4cn5, assembly 1, side view.
5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3' in PDB entry 4cn5, assembly 1, top view.
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