6L6K: Dimeric RXRalpha-LBD

Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Nov 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,979
Mol. weight: 28.96 kDa
Ligands: CA, 9HF
Released: 4 Nov 2020

Explore 6L6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L6K contains 14 α-helices and 2 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	232-241	10
α-helix	264-285	22
α-helix	289-291	3
α-helix	294-316	23
β-strand	323-325	3	1
β-strand	331-333	3	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 1	B	protein	12	Homo sapiens	Q15788 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6L6K_1 Retinoic acid receptor RXR-alpha (chains A)
GSSHSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTL
VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHS
AGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYAS
LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPH
QMT

Sequence of entity 2 (B), FASTA

>6L6K_2 Nuclear receptor coactivator 1 (chains B)
HKILHRLLQEGS

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
9HF	1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic…	C22 H25 N3 O2	1

Primary citation

Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1. Shimizu, K., 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…
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
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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