1MZN: RXR retinoid X receptor

Crystal structure at 1.9 angstroems resolution of the homodimer of human rxr alpha ligand binding domain bound to the synthetic agonist compound bms 649 and a coactivator peptide. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Oct 2002.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 8,177
Mol. weight: 115.26 kDa
Ligands: BM6
Released: 23 Oct 2002

Explore 1MZN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1MZN contains 61 α-helices and 8 β-strands across 8 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: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	232-241	10
α-helix	243-245	3
α-helix	246-250	5
α-helix	264-284	21
α-helix	289-291	3
α-helix	294-316	23
α-helix	317-319	3
β-strand	324-325	2	1
β-strand	331-332	2	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	386-407	22
α-helix	414-419	6
α-helix	422-442	21
α-helix	449-455	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	473-480	8

Chain C: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1232-1242	11
α-helix	1264-1285	22
α-helix	1289-1291	3
α-helix	1294-1316	23
β-strand	1323-1325	3	2
β-strand	1331-1333	3	2
α-helix	1334-1339	6
α-helix	1343-1348	6
α-helix	1349-1354	6
α-helix	1355-1359	5
α-helix	1364-1375	12
α-helix	1386-1407	22
α-helix	1414-1419	6
α-helix	1422-1442	21
α-helix	1449-1454	6

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1473-1480	8

Chain E: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2232-2241	10
α-helix	2243-2245	3
α-helix	2246-2252	7
α-helix	2264-2284	21
α-helix	2289-2291	3
α-helix	2294-2316	23
α-helix	2317-2319	3
β-strand	2324-2325	2	3
β-strand	2331-2332	2	3
α-helix	2334-2339	6
α-helix	2343-2348	6
α-helix	2349-2354	6
α-helix	2355-2360	6
α-helix	2364-2375	12
α-helix	2386-2407	22
α-helix	2414-2419	6
α-helix	2422-2442	21
α-helix	2449-2455	7

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2473-2480	8

Chain G: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3232-3242	11
α-helix	3264-3285	22
α-helix	3294-3316	23
β-strand	3323-3325	3	4
β-strand	3331-3333	3	4
α-helix	3334-3340	7
α-helix	3343-3348	6
α-helix	3349-3354	6
α-helix	3355-3359	5
α-helix	3364-3375	12
α-helix	3386-3407	22
α-helix	3414-3419	6
α-helix	3422-3442	21
α-helix	3449-3455	7

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3473-3480	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RXR retinoid X receptor	A, C, E, G	protein	240	Homo sapiens	P19793 (AlphaFold model)
Nuclear receptor coactivator 2	B, D, F, H	protein	13	synthetic construct	Q15596 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>1MZN_1 RXR retinoid X receptor (chains A, C, E, G)
TSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEW
AKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV
GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA
YCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT

Sequence of entity 2 (B, D, F, H), FASTA

>1MZN_2 Nuclear receptor coactivator 2 (chains B, D, F, H)
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	4

Primary citation

Molecular Recognition of Agonist Ligands by RXRs. Egea, P.F., Mitschler, A., Moras, D. Mol Endocrinol (2002) 16:987-997. DOI 10.1210/me.16.5.987 · 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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