3AFR: Vitamin D3 receptor

Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 31 Mar 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Rattus norvegicus, Xenopus tropicalis
Chains: 2
Atoms: 2,109
Mol. weight: 32.64 kDa
Ligands: ICJ
Released: 31 Mar 2010

Explore 3AFR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AFR contains 16 α-helices and 3 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	126-140	15
α-helix	148-152	5
α-helix	154-156	3
α-helix	223-242	20
α-helix	247-249	3
α-helix	252-270	19
α-helix	271-273	3
β-strand	275-276	2	1
β-strand	281-283	3	1
α-helix	287-289	3
β-strand	290-291	2	1
α-helix	293-297	5
α-helix	303-317	15
α-helix	323-334	12
α-helix	345-366	22
α-helix	375-400	26
α-helix	404-407	4
α-helix	412-418	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	628-634	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin D3 receptor	A	protein	271	Rattus norvegicus	P13053 (AlphaFold model)
13-meric peptide from Mediator of RNA polymerase II transcription subunit 1	C	protein	13	Xenopus tropicalis	A1L0Z0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3AFR_1 Vitamin D3 receptor (chains A)
GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGS
VTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSN
QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEE
HSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (C), FASTA

>3AFR_2 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (chains C)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
ICJ	(1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethyl…	C31 H52 O3	1

Primary citation

22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity. Inaba, Y., Nakabayashi, M., Itoh, T. et al. J Steroid Biochem Mol Biol (2010) 121:146-150. DOI 10.1016/j.jsbmb.2010.02.033 · PubMed

Other PDB entries of the same protein (UniProt P13053 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9VOG 1.43 Å, Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid…
9M1D 1.44 Å, Vitamin D receptor complex with a methyldiphenylpropylsilane derivative
3VTC 1.5 Å, Crystal structure of rat vitamin D receptor bound to a partial agonist…
3VT7 1.65 Å, Crystal structures of rat VDR-LBD with W282R mutation
9M1C 1.67 Å, Vitamin D receptor complex with a triphenylpropylsilane derivative
9M13 1.68 Å, Vitamin D receptor complex with a dimethyldiphenylsilane derivative
2ZMI 1.7 Å, Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs:…
3VT3 1.7 Å, Crystal structures of rat VDR-LBD with R270L mutation
2O4J 1.74 Å, Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII…
9VOL 1.75 Å, Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid…
9M1B 1.77 Å, Vitamin D receptor complex with a diphenydipropylsilane derivative
9M1A 1.78 Å, Vitamin D receptor complex with a diethyldiphenylsilane derivative

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