7PDT: Mutated form of RXRalpha ligand binding domain

Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with BMS649 and a coactivator fragment. Determined by X-ray diffraction at 3.3 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 3,491
Mol. weight: 58.3 kDa
Ligands: BM6
Released: 3 Aug 2022

Explore 7PDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PDT contains 28 α-helices and 4 β-strands across 4 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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	237-246	10
α-helix	269-289	21
α-helix	299-321	23
β-strand	328-330	3	1
β-strand	336-338	3	1
α-helix	339-344	6
α-helix	348-353	6
α-helix	354-359	6
α-helix	360-364	5
α-helix	369-380	12
α-helix	391-412	22
α-helix	419-424	6
α-helix	426-447	22
α-helix	454-459	6

Chain B: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	237-245	9
α-helix	269-289	21
α-helix	299-306	8
α-helix	310-321	12
β-strand	328-330	3	2
α-helix	335	1
β-strand	336-338	3	2
α-helix	339-344	6
α-helix	348-353	6
α-helix	354-359	6
α-helix	360-364	5
α-helix	369-380	12
α-helix	391-412	22
α-helix	419-424	6
α-helix	427-447	21
α-helix	454-458	5

Chain U: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	252-259	8

Chain V: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	303-306	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A, B	protein	245	Mus musculus	P28700 (AlphaFold model)
Nuclear receptor coactivator 2	U, V	protein	13	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7PDT_1 Retinoic acid receptor RXR-alpha (chains A, B)
GPHMSTSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLF
TLVEWAKRIPHFSELPLDDQVILLRAGWNELLAASASHRSIAVKDGILLTTGLHVHRNSA
HSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVY
ASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA
PHQAT

Sequence of entity 2 (U, V), FASTA

>7PDT_2 Nuclear receptor coactivator 2 (chains U, V)
KHKILHRLLQDSS

Ligands and cofactors

ID	Name	Formula	Copies
BM6	4-[2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-naphthalen-2-yl)-[1,3]DIOXOLAN-2-Y…	C24 H27 O4	2

Primary citation

Design and in vitro characterization of RXR variants as tools to investigate the biological role of endogenous rexinoids. le Maire, A., Rey, M., Vivat, V. et al. J Mol Endocrinol (2022) 69:377-390. DOI 10.1530/JME-22-0021 · PubMed

Other PDB entries of the same protein (UniProt P28700 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PDQ 1.58 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…
1DKF 2.5 Å, Crystal structure of a heterodimeric complex of rar and rxr ligand-binding domains
7AOS 2.55 Å, crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex…
8J54 2.72 Å, Crystal structure of RXR/DR2 complex
3A9E 2.75 Å, Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha…
7QAA 2.76 Å, Crystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with…
1XDK 2.9 Å, Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex…

Browse structure collections

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