6FBQ: Human Retinoid X Receptor DNA-Binding Domain

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human MEp DR1 Response Element, pH 7.0. Determined by X-ray diffraction at 1.6 Å resolution. Released 5 Dec 2018.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,674
Mol. weight: 31.41 kDa
Ligands: MPO, ZN
Released: 5 Dec 2018

Explore 6FBQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FBQ contains 10 α-helices and 8 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	133-134	2	1
β-strand	141-142	2	1
β-strand	145-146	2	2
β-strand	149-150	2	2
α-helix	153-164	12
α-helix	188-198	11
α-helix	202-204	3
α-helix	206-208	3

Chain B: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	134	1	3
β-strand	141	1	3
α-helix	142	1
β-strand	144-146	3	4
β-strand	149-151	3	4
α-helix	153-164	12
α-helix	184-186	3
α-helix	188-197	10
α-helix	202-204	3
α-helix	207-210	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A, B	protein	87	Homo sapiens	P19793 (AlphaFold model)
DNA (5'-d(cptpgpgpgptpcpapapapgptptpcpaptp*c)-3')	C	DNA	17	Homo sapiens
DNA (5'-d(gpaptpgpapapcptptptpgpapcpcpcpap*g)-3')	D	DNA	17	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6FBQ_1 Retinoic acid receptor RXR-alpha (chains A, B)
GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRN
RCQYCRYQKCLAMGMKREAVQEERQRG

Sequence of entity 2 (C), FASTA

>6FBQ_2 DNA (5'-D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3') (chains C)
CTGGGTCAAAGTTCATC

Sequence of entity 3 (D), FASTA

>6FBQ_3 DNA (5'-D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3') (chains D)
GATGAACTTTGACCCAG

Ligands and cofactors

ID	Name	Formula	Copies
MPO	3[N-morpholino]propane sulfonic acid	C7 H15 N O4 S	1
ZN	Zinc ion	Zn	4

Primary citation

Modulation of RXR-DNA complex assembly by DNA context. Osz, J., McEwen, A.G., Wolf, J. et al. Mol Cell Endocrinol (2019) 481:44-52. DOI 10.1016/j.mce.2018.11.008 · PubMed

Other PDB entries of the same protein (UniProt P19793 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QX6 1.46 Å, Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator…
6LB4 1.5 Å, Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator
7A77 1.5 Å, Crystal structure of RXR alpha LBD in complexes with palmitic acid and GRIP-1 peptide
9RMR 1.65 Å, Crystal structure of RXR alpha LBD bound to a synthetic agonist FN558 and a coactivator…
1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
5MKU 1.78 Å, Crystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol…
2P1T 1.8 Å, Crystal structure of the ligand binding domain of the retinoid X receptor alpha in…
4ZSH 1.8 Å, RXR LBD in complex with 9-cis-13,14-dihydroretinoic acid
6L6K 1.8 Å, Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1
7UW2 1.88 Å, Crystal structure of human Retinoid X receptor alpha ligand binding domain complex with…
6STI 1.89 Å, Crystal structure of RXRalpha LBD in complex with LG 100754 and a coactivator peptide
1MV9 1.9 Å, Crystal Structure of the human RXR alpha ligand binding domain bound to the eicosanoid…

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