1DSZ: Rxr/rar DNA-binding domain heterodimer

Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic acid response element DR1. Determined by X-ray diffraction at 1.7 Å resolution. Released 10 Jul 2000.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,193
Mol. weight: 29.65 kDa
Ligands: ZN
Released: 10 Jul 2000

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

Secondary structure: helices and β-sheets

1DSZ contains 8 α-helices and 6 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1141-1142	2
β-strand	1145-1146	2	1
β-strand	1149-1150	2	1
α-helix	1153-1164	12
α-helix	1184-1186	3
α-helix	1188-1197	10
α-helix	1202-1204	3

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	1233-1234	2	2
β-strand	1241-1242	2	2
β-strand	1245-1246	2	3
β-strand	1249-1250	2	3
α-helix	1253-1265	13
α-helix	1288-1297	10
α-helix	1302-1304	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(cpapgpgptpcpapapapgpgptpcpap*g)-3')	C	DNA	15
DNA (5'-d(cptpgpapcpcptptptpgpapcpcptp*g)-3')	D	DNA	15
Retinoic acid receptor alpha	A	protein	86	Homo sapiens	P10276 (AlphaFold model)
Retinoic acid receptor rxr-alpha	B	protein	85	Homo sapiens	P19793 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>1DSZ_1 DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') (chains C)
CAGGTCAAAGGTCAG

Sequence of entity 2 (D), FASTA

>1DSZ_2 DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3') (chains D)
CTGACCTTTGACCTG

Sequence of entity 3 (A), FASTA

>1DSZ_3 RETINOIC ACID RECEPTOR ALPHA (chains A)
PRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQ
YCRLQKCFEVGMSKESVRNDRNKKKK

Sequence of entity 4 (B), FASTA

>1DSZ_4 RETINOIC ACID RECEPTOR RXR-ALPHA (chains B)
GSFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRC
QYCRYQKCLAMGMKREAVQEERQRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1. Rastinejad, F., Wagner, T., Zhao, Q. et al. EMBO J (2000) 19:1045-1054. DOI 10.1093/emboj/19.5.1045 · 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
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…
4DQM 2.75 Å, Revealing a marine natural product as a novel agonist for retinoic acid receptors with a…

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