7APO: RARalpha ligand binding domain

Crystal structure of RARalpha ligand binding domain in complex with a fragment of the TIF2 coactivator. Determined by X-ray diffraction at 2.4 Å resolution. Released 4 Aug 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,228
Mol. weight: 63.17 kDa
Ligands: EQN
Released: 4 Aug 2021

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

Secondary structure: helices and β-sheets

7APO contains 32 α-helices and 10 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: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	184-198	15
α-helix	205-207	3
β-strand	208	1	1
α-helix	222-244	23
α-helix	249-251	3
α-helix	254-275	22
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	373-399	27
α-helix	408-413	6

Chain B: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	183-198	16
α-helix	202-204	3
β-strand	208	1	3
α-helix	222-245	24
α-helix	249-251	3
α-helix	254-274	21
β-strand	277-278	2	4
β-strand	283-285	3	4
β-strand	290	1	3
β-strand	291-293	3	4
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	408-413	6

Chains C and D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	688-694	7
α-helix	700-711	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor alpha	A, B	protein	249	Homo sapiens	P10276 (AlphaFold model)
Nuclear receptor coactivator 2	C, D	protein	28	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7APO_1 Retinoic acid receptor alpha (chains A, B)
GSHESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELS
TKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTL
NRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQ
EPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQE
MLENSEGLD

Sequence of entity 2 (C, D), FASTA

>7APO_2 Nuclear receptor coactivator 2 (chains C, D)
KHKILHRLLQDSSSPVDLAKLTAEATGK

Ligands and cofactors

ID	Name	Formula	Copies
EQN	4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzo…	C22 H25 N O3	2

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

Primary citation

Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR). Senicourt, L., le Maire, A., Allemand, F. et al. J Mol Biol (2021) 433:166899-166899. DOI 10.1016/j.jmb.2021.166899 · 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
3KMZ 2.1 Å, Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist…
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…
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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