8J54: RXR/DR2 complex

Crystal structure of RXR/DR2 complex. Determined by X-ray diffraction at 2.72 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 2.72 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 3,957
Mol. weight: 61.99 kDa
Ligands: ZN
Released: 17 Jan 2024

Explore 8J54 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J54 contains 13 α-helices and 16 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 C: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	138	1	1
α-helix	144	1
β-strand	145	1	1
α-helix	146	1
β-strand	149-150	2	2
β-strand	153-154	2	2
α-helix	157-169	13
α-helix	192-201	10
α-helix	210-212	3

Chain D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	138	1	3
β-strand	145	1	3
β-strand	149-150	2	4
β-strand	153-154	2	4
α-helix	157-168	12
α-helix	192-201	10
α-helix	210-211	2

Chain E: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	138	1	5
β-strand	145	1	5
β-strand	149-150	2	6
β-strand	153-154	2	6
α-helix	157-168	12
α-helix	192-201	10

Chain F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	138	1	7
β-strand	145	1	7
β-strand	149-150	2	8
β-strand	153-154	2	8
α-helix	157-168	12
α-helix	192-202	11
α-helix	210-212	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(cpaptpgpapcpcptpapcptpgpapcpcptpapg)-3')	A, N	DNA	18	Homo sapiens
DNA (5'-d(cptpapgpgptpcpapgptpapgpgptpcpaptpg)-3')	B, P	DNA	18	Homo sapiens
Retinoic acid receptor RXR	C, D, E, F	protein	83	Mus musculus	P28700 (AlphaFold model)

Sequence of entity 1 (A, N), FASTA

>8J54_1 DNA (5'-D(*CP*AP*TP*GP*AP*CP*CP*TP*AP*CP*TP*GP*AP*CP*CP*TP*AP*G)-3') (chains A, N)
CATGACCTACTGACCTAG

Sequence of entity 2 (B, P), FASTA

>8J54_2 DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*GP*TP*AP*GP*GP*TP*CP*AP*TP*G)-3') (chains B, P)
CTAGGTCAGTAGGTCATG

Sequence of entity 3 (C, D, E, F), FASTA

>8J54_3 Retinoic acid receptor RXR (chains C, D, E, F)
FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY
CRYQKCLAMGMKREAVQEERQRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma. Jiang, L., Liu, X., Liang, X. et al. Structure (2024) 32:467-475.e3. DOI 10.1016/j.str.2024.01.004 · PubMed

Other PDB entries of the same protein (UniProt P28700 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PDQ 1.58 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…
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…
7QAA 2.76 Å, Crystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with…
1XDK 2.9 Å, Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex…
7PDT 3.3 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…

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