4RMD: Retinoic acid receptor RXR-alpha

Crystal structure of human Retinoid X receptor alpha ligand binding domain complex with 9cUAB110 and coactivator peptide GRIP-1. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Sept 2015.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,937
Mol. weight: 28.33 kDa
Ligands: 3SW
Released: 23 Sept 2015

Explore 4RMD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RMD contains 14 α-helices and 2 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	232-242	11
α-helix	264-284	21
α-helix	289-291	3
α-helix	294-316	23
β-strand	323-325	3	1
β-strand	331-333	3	1
α-helix	334-339	6
α-helix	343-348	6
α-helix	349-354	6
α-helix	355-360	6
α-helix	364-375	12
α-helix	386-406	21
α-helix	414-419	6
α-helix	422-442	21
α-helix	449-454	6

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	473-480	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A	protein	235	Homo sapiens	P19793 (AlphaFold model)
Nuclear receptor coactivator 2	B	protein	13	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4RMD_1 Retinoic acid receptor RXR-alpha (chains A)
EDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIP
HFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFD
RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHK
YPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT

Sequence of entity 2 (B), FASTA

>4RMD_2 Nuclear receptor coactivator 2 (chains B)
KHKILHRLLQDSS

Ligands and cofactors

ID	Name	Formula	Copies
3SW	(2E,4E,6Z,8E)-8-[3-cyclopropyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-di…	C24 H34 O2	1

Primary citation

Conformationally Defined Rexinoids and Their Efficacy in the Prevention of Mammary Cancers. Atigadda, V.R., Xia, G., Deshpande, A. et al. J Med Chem (2015) 58:7763-7774. DOI 10.1021/acs.jmedchem.5b00829 · PubMed

Other PDB entries of the same protein (UniProt P19793 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QX6 1.46 Å, Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator…
6LB4 1.5 Å, Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator
7A77 1.5 Å, Crystal structure of RXR alpha LBD in complexes with palmitic acid and GRIP-1 peptide
6FBQ 1.6 Å, Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human…
9RMR 1.65 Å, Crystal structure of RXR alpha LBD bound to a synthetic agonist FN558 and a coactivator…
1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
5MKU 1.78 Å, Crystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol…
2P1T 1.8 Å, Crystal structure of the ligand binding domain of the retinoid X receptor alpha in…
4ZSH 1.8 Å, RXR LBD in complex with 9-cis-13,14-dihydroretinoic acid
6L6K 1.8 Å, Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1
7UW2 1.88 Å, Crystal structure of human Retinoid X receptor alpha ligand binding domain complex with…
6STI 1.89 Å, Crystal structure of RXRalpha LBD in complex with LG 100754 and a coactivator peptide

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