4DQM: Retinoic acid receptor alpha

Revealing a marine natural product as a novel agonist for retinoic acid receptors with a unique binding mode and antitumor activity. Determined by X-ray diffraction at 2.75 Å resolution. Released 3 Oct 2012.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,940
Mol. weight: 56.09 kDa
Ligands: LUF
Released: 3 Oct 2012

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

Secondary structure: helices and β-sheets

4DQM contains 31 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: 16 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	183-198	16
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	380-389	10
α-helix	391-401	11
α-helix	408-414	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1434-1440	7

Chain C: 13 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	222-244	23
α-helix	249-251	3
α-helix	254-274	21
β-strand	277	1	4
β-strand	284-285	2	4
β-strand	290	1	3
β-strand	291-292	2	4
α-helix	294-297	4
α-helix	298-302	5
α-helix	305-315	11
α-helix	323-334	12
α-helix	345-366	22
α-helix	373-389	17
α-helix	391-399	9
α-helix	408-414	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1436-1439	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor alpha	A, C	protein	234	Homo sapiens	P10276 (AlphaFold model)
Nuclear receptor coactivator 1	B, D	protein	10	Homo sapiens	Q15788 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4DQM_1 Retinoic acid receptor alpha (chains A, C)
PEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVE
FAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAG
FGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKV
YVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLE

Sequence of entity 2 (B, D), FASTA

>4DQM_2 Nuclear receptor coactivator 1 (chains B, D)
KSLLQQLLTE

Ligands and cofactors

ID	Name	Formula	Copies
LUF	(5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethylcyclohex-1-en-1-yl)deca-3,7-die…	C25 H38 O3	2

Primary citation

Revealing a natural marine product as a novel agonist for retinoic acid receptors with a unique binding mode and inhibitory effects on cancer cells. Wang, S., Wang, Z., Lin, S. et al. Biochem J (2012) 446:79-87. DOI 10.1042/BJ20120726 · 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…
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…

Browse structure collections

About this viewer

MolViewer shows 4DQM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.