3A9E: Retinoic acid receptor RXR-alpha

Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha heterodimer ligand binding domains. Determined by X-ray diffraction at 2.75 Å resolution. Released 6 Oct 2010.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Mus musculus, Homo sapiens, HOMO SAPIENS
Chains: 3
Atoms: 3,877
Mol. weight: 59.55 kDa
Ligands: 754, REA
Released: 6 Oct 2010

Explore 3A9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3A9E contains 28 α-helices and 7 β-strands across 3 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: 14 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	427-440	14
α-helix	442-445	4
α-helix	451-453	3
α-helix	454-460	7

Chain B: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	182-198	17
β-strand	208	1	2
α-helix	222-244	23
α-helix	254-273	20
α-helix	274-276	3
β-strand	277-278	2	3
β-strand	283-285	3	3
β-strand	290	1	2
β-strand	291-293	3	3
α-helix	294-297	4
α-helix	298-302	5
α-helix	303-305	3
α-helix	306-316	11
α-helix	317-319	3
α-helix	323-334	12
α-helix	345-366	22
α-helix	373-401	29
α-helix	408-414	7

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1473-1480	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A	protein	240	Mus musculus	P28700 (AlphaFold model)
Retinoic acid receptor alpha	B	protein	269	Homo sapiens	P10276 (AlphaFold model)
13-mer (LXXLL motif) from Nuclear receptor coactivator 2	I	protein	13	HOMO SAPIENS	Q15596 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3A9E_1 Retinoic acid receptor RXR-alpha (chains A)
TSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEW
AKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV
GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA
YCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQAT

Sequence of entity 2 (B), FASTA

>3A9E_2 Retinoic acid receptor alpha (chains B)
MSKESVRNDRNKKKKEVPKPECSESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNN
SSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILR
ICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAI
CLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGA
ERVITLKMEIPGSMPPLIQEMLENSEGLD

Sequence of entity 3 (I), FASTA

>3A9E_3 13-mer (LXXLL motif) from Nuclear receptor coactivator 2 (chains I)
KHKILHRLLQDSS

Ligands and cofactors

ID	Name	Formula	Copies
754	(2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5,6,7,8-tetrahydronaphthal…	C26 H36 O3	1
REA	Retinoic acid	C20 H28 O2	1

Primary citation

The Phantom Effect of the Rexinoid LG100754: structural and functional insights. Sato, Y., Ramalanjaona, N., Huet, T. et al. PLoS One (2010) 5:e15119-e15119. DOI 10.1371/journal.pone.0015119 · 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
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…
7PDT 3.3 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…

Browse structure collections

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