3KMZ: RARalpha ligand binding domain

Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Jun 2010.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,262
Mol. weight: 66.07 kDa
Ligands: EQO
Released: 2 Jun 2010

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

Secondary structure: helices and β-sheets

3KMZ contains 29 α-helices and 14 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: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	182-198	17
α-helix	202-204	3
β-strand	208	1	4
α-helix	222-244	23
α-helix	249-251	3
α-helix	254-275	22
β-strand	277-278	2	5
β-strand	283-285	3	5
β-strand	290	1	4
β-strand	291-293	3	5
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	373-392	20
β-strand	395-397	3	6

Chain B: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	182-198	17
α-helix	202-204	3
β-strand	208	1	1
α-helix	222-244	23
α-helix	249-251	3
α-helix	254-274	21
β-strand	277-278	2	2
β-strand	283-285	3	2
β-strand	290	1	1
β-strand	291-293	3	2
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	373-378	6
α-helix	380-392	13
β-strand	395-397	3	3

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2048-2050	3	3
α-helix	2051-2063	13

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2048-2050	3	6
α-helix	2051-2062	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor alpha	A, B	protein	266	Homo sapiens	P10276 (AlphaFold model)
Nuclear receptor corepressor 1	C, D	protein	19		O75376 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3KMZ_1 Retinoic acid receptor alpha (chains A, B)
MGSSHHHHHHSSGLVPRGSHESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSE
QRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICT
RYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLI
CGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERV
ITLKMEIPGSMPPLIQEMLENSEGLD

Sequence of entity 2 (C, D), FASTA

>3KMZ_2 Nuclear receptor corepressor 1 (chains C, D)
RLITLADHICQIITQDFAR

Ligands and cofactors

ID	Name	Formula	Copies
EQO	4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}ben…	C29 H24 O2	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor. le Maire, A., Teyssier, C., Erb, C. et al. Nat Struct Mol Biol (2010) 17:801-807. DOI 10.1038/nsmb.1855 · PubMed

Other PDB entries of the same protein (UniProt P10276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GFE 1.58 Å, hRAR LBD protein in complex with AM580 agonist ligand and a stapled peptide
1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
3KMR 1.8 Å, Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand…
5K13 1.85 Å, Crystal structure of the RAR alpha ligand-binding domain in complex with an antagonist
7WQQ 1.9 Å, Retinoic acid receptor alpha mutant - N299H
9GFI 2.1 Å, hRAR alpha LBD-AM580 complex with staple peptide
6XWG 2.4 Å, Crystal Structure of the Human RXR/RAR DNA-Binding Domain Heterodimer Bound to the Human…
7APO 2.4 Å, Crystal structure of RARalpha ligand binding domain in complex with a fragment of the…
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…
3A9E 2.75 Å, Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha…
4DQM 2.75 Å, Revealing a marine natural product as a novel agonist for retinoic acid receptors with a…

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