8FKG: PPARgamma ligand-binding domain

Name: PDB 8FKG: Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33486
Published: 2024-04-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33486. Determined by X-ray diffraction at 2.12 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,407
Mol. weight: 35.13 kDa
Ligands: Y62
Released: 17 Apr 2024

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

Secondary structure: helices and β-sheets

8FKG contains 16 α-helices and 4 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: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	206-225	20
α-helix	230-237	8
α-helix	246	1
β-strand	247-249	3	1
α-helix	252-257	6
α-helix	277-288	12
α-helix	290-301	12
α-helix	311-332	22
β-strand	334-335	2	1
β-strand	338-341	4	1
β-strand	346-349	4	1
α-helix	350-355	6
α-helix	357	1
α-helix	360-362	3
α-helix	365-375	11
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-458	28
α-helix	467-473	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2260-2270	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear receptor corepressor 1	D	protein	23	Homo sapiens	O75376 (AlphaFold model)
Peroxisome proliferator-activated receptor gamma	A	protein	276	Homo sapiens	P37231 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>8FKG_1 Nuclear receptor corepressor 1 (chains D)
DPASNLGLEDIIRKALMGSFDDK

Sequence of entity 2 (A), FASTA

>8FKG_2 Peroxisome proliferator-activated receptor gamma (chains A)
GQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDK
IKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYG
VHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDD
SDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTD
LRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Ligands and cofactors

ID	Name	Formula	Copies
Y62	2-chloro-N-(5-cyanopyridin-2-yl)-5-nitrobenzamide	C13 H7 Cl N4 O3	1

Water and common crystallization additives (K, EDO, SO4, GOL) are not listed.

Primary citation

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states. MacTavish, B.S., Zhu, D., Shang, J. et al. Nat Commun (2025) 16:2065-2065. DOI 10.1038/s41467-025-57325-4 · PubMed

Other PDB entries of the same protein (UniProt O75376 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XZZ 1.39 Å, Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD2 peptide
8FKC 1.42 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
6XYX 1.44 Å, Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide
6Y17 1.56 Å, Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with nebulinSH3-NCoR1BBD1
8DKV 1.59 Å, PPARg bound to JTP-426467 and Co-R peptide
6ONI 1.8 Å, Crystal structure of PPARgamma ligand binding domain in complex with N-CoR peptide and…
8FHE 1.8 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
8FHG 1.8 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
8FKF 1.82 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
8DKN 1.95 Å, PPARg bound to T0070907 and Co-R peptide
6WMS 2.0 Å, Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR…
8FKE 2.02 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…

Browse structure collections

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