6XWG: Human RXR/RAR DNA-Binding Domain Heterodimer

Crystal Structure of the Human RXR/RAR DNA-Binding Domain Heterodimer Bound to the Human RARb2 DR5 Response Element. Determined by X-ray diffraction at 2.4 Å resolution. Released 9 Sept 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,197
Mol. weight: 34.17 kDa
Ligands: ZN
Released: 9 Sept 2020

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

Secondary structure: helices and β-sheets

6XWG 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 C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	133-134	2	1
β-strand	141-142	2	1
β-strand	144-146	3	2
β-strand	149-151	3	2
α-helix	153-164	12
α-helix	188-197	10
α-helix	202-204	3
α-helix	206-208	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	94-95	2
β-strand	97-99	3	3
β-strand	102-104	3	3
α-helix	106-117	12
α-helix	141-151	11
α-helix	155-157	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RARb2 DR5 Response Element, 5'-3' strand	A	DNA	21	Homo sapiens
RARb2 DR5 Response Element, 3'-5' strand	B	DNA	21	Homo sapiens
Retinoic acid receptor RXR-alpha	C	protein	87	Homo sapiens	P19793 (AlphaFold model)
Retinoic acid receptor alpha	D	protein	90	Homo sapiens	P10276 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XWG_1 RARb2 DR5 Response Element, 5'-3' strand (chains A)
AGGGTTCACCGAAAGTTCACT

Sequence of entity 2 (B), FASTA

>6XWG_2 RARb2 DR5 Response Element, 3'-5' strand (chains B)
AGTGAACTTTCGGTGAACCCT

Sequence of entity 3 (C), FASTA

>6XWG_3 Retinoic acid receptor RXR-alpha (chains C)
GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRN
RCQYCRYQKCLAMGMKREAVQEERQRG

Sequence of entity 4 (D), FASTA

>6XWG_4 Retinoic acid receptor alpha (chains D)
GSHMPRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTR
NRCQYCRLQKCFEVGMSKESVRNDRNKKKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR. Osz, J., McEwen, A.G., Bourguet, M. et al. Nucleic Acids Res (2020) 48:9969-9985. DOI 10.1093/nar/gkaa697 · 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
6FBQ 1.6 Å, Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human…
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

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