6LB4: Dimeric RXR-LBD

Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator. Determined by X-ray diffraction at 1.5 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,150
Mol. weight: 29.31 kDa
Ligands: E8L
Released: 18 Nov 2020

Explore 6LB4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LB4 contains 15 α-helices and 3 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: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	232-242	11
β-strand	250-251	2	1
α-helix	264-284	21
α-helix	289-291	3
α-helix	294-316	23
α-helix	317-319	3
β-strand	323-325	3	1
β-strand	330-333	4	1
α-helix	334-339	6
α-helix	343-348	6
α-helix	349-354	6
α-helix	355-360	6
α-helix	364-375	12
α-helix	386-407	22
α-helix	414-419	6
α-helix	422-442	21
α-helix	449-454	6

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	688-694	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor RXR-alpha	A	protein	243	Homo sapiens	P19793 (AlphaFold model)
Nuclear receptor coactivator 2	B	protein	13	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6LB4_1 Retinoic acid receptor RXR-alpha (chains A)
GSSHSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTL
VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHS
AGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYAS
LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPH
QMT

Sequence of entity 2 (B), FASTA

>6LB4_2 Nuclear receptor coactivator 2 (chains B)
KHKILHRLLQDSS

Ligands and cofactors

ID	Name	Formula	Copies
E8L	6-[ethyl-[3-(2-methoxyethoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic…	C20 H26 N2 O4	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator. Imai, D., Numoto, N., Nakano, S. et al. To be published.

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…
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
1MV9 1.9 Å, Crystal Structure of the human RXR alpha ligand binding domain bound to the eicosanoid…

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