8FKD: PPARgamma ligand-binding domain

Name: PDB 8FKD: Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33068
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 SR33068. Determined by X-ray diffraction at 2.22 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.22 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,384
Mol. weight: 34.5 kDa
Ligands: Y5O
Released: 17 Apr 2024

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

Secondary structure: helices and β-sheets

8FKD contains 14 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: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	206-225	20
α-helix	230-237	8
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	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	467-474	8

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2261-2271	11

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>8FKD_1 Peroxisome proliferator-activated receptor gamma (chains A)
GQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDK
IKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYG
VHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDD
SDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTD
LRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (D), FASTA

>8FKD_2 Nuclear receptor corepressor 1 (chains D)
DPASNLGLEDIIRKALMGSFDDK

Ligands and cofactors

ID	Name	Formula	Copies
Y5O	2-chloro-N-(6-cyanopyridin-3-yl)-5-nitrobenzamide	C13 H7 Cl N4 O3	1

Water and common crystallization additives (EDO) 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 P37231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F7W 1.25 Å, Human PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and…
8BF1 1.36 Å, High-resolution structure of unliganded PPAR gamma in complex with the peptide PGC-1 alpha
9V8G 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL
9V8H 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone
8FKC 1.42 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
6MS7 1.43 Å, Peroxisome proliferator-activated receptor gamma ligand binding domain in complex with a…
9V8D 1.44 Å, PPARgamma ligand-binding domain in complex with PG08
3U9Q 1.52 Å, Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide
8B94 1.55 Å, Crystal structure of PPARG and NCOR2 with BAY-5516, an inverse agonist
8DKV 1.59 Å, PPARg bound to JTP-426467 and Co-R peptide
3B1M 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…
3V9V 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…

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