4rwv

Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution

Method: X-RAY DIFFRACTION D_max: 66.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear receptor subfamily 5 group A member 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–248	Fragment：LIGAND BINDING DOMAIN (UNP residues 294-551) Non-standard monomer：Yes (specific site not provided by mmCIF)	Nuclear receptor DAX1 × 1 （F1D8P4） PIZ (2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dihexadecanoate × 1 EDO 1,2-ETHANEDIOL × 5 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；LRH-1/PIP3, 20% PEG 4K, 0.2M NaOAc, 0.1M Tris (8.5), 0.036mM PIP3, 0.90mM 15-mer PRQGSILYSLLTSSK, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.86 Å R-free 0.210

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4RWV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YOK crystal structure of human LRH-1 bound with TIF-2 peptide and phosphatidylglycerol Deposited 2005-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 300–541（242 aa） Fragment：sequence database residues 300-541: contains ligand binding domain (residues 346-388)	Not recorded	P6L (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；298 K；Sodium potassium phosphate, glycerol, ethylene glycol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.290
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 290–541（252 aa） Fragment：Ligand Binding Domain	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 290–541（252 aa） Fragment：Ligand Binding Domain	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 290–541（252 aa） Fragment：Ligand Binding Domain Chain B 290–541（252 aa） Fragment：Ligand Binding Domain	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 290–541（252 aa） Fragment：Ligand Binding Domain Chain B 290–541（252 aa） Fragment：Ligand Binding Domain	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1ZDU The Crystal Structure of Human Liver Receptor Homologue-1 Deposited 2005-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 297–541（245 aa）	Not recorded	P3A PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NaH2PO4, K2HPO4, pH 7.5, temperature 293K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.50 Å R-free 0.281
2A66 Human Liver Receptor Homologue DNA-Binding Domain (hLRH-1 DBD) in Complex with dsDNA from the hCYP7A1 Promoter Deposited 2005-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 79–187（109 aa） Fragment：residues 79-187, NR C4-type	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；295 K；magnesium acetate, ammonium acetate, sodium cacodylate, PEG 8000, glycerol, sodium azide, hexaamine cobalt (III) trichloride, pH 6.0, hanging drop, temperature 295K, pH 6.00	Resolution 2.20 Å R-free 0.226
3TX7 Crystal structure of LRH-1/beta-catenin complex Deposited 2011-09-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 191–541（351 aa）	Not recorded	P6L (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20 mM Tris-HCl, 40% PEG200, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.76 Å R-free 0.243
4DOR Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1 Deposited 2012-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 290–541（252 aa） Fragment：UNP residues 290-541 Chain B 290–541（252 aa） Fragment：UNP residues 290-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.220
4DOR Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1 Deposited 2012-02-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 290–541（252 aa） Fragment：UNP residues 290-541	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.220
4DOR Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1 Deposited 2012-02-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 290–541（252 aa） Fragment：UNP residues 290-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.220
4DOS Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to DLPC and a Fragment of TIF-2 Deposited 2012-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 299–538（240 aa） Fragment：Ligand Binding Domain, UNP residues 299-538	Not recorded	1PE PENTAETHYLENE GLYCOL × 3 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5.2；298 K；18%-24% PEG 400, 5% glycerol, 0.1M lithium sulfate, and 0.1M sodium acetate pH 5.2, hanging drop vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.238
4DOS Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to DLPC and a Fragment of TIF-2 Deposited 2012-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 299–538（240 aa） Fragment：Ligand Binding Domain, UNP residues 299-538	Not recorded	1PE PENTAETHYLENE GLYCOL × 3 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5.2；298 K；18%-24% PEG 400, 5% glycerol, 0.1M lithium sulfate, and 0.1M sodium acetate pH 5.2, hanging drop vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.238
4DOS Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to DLPC and a Fragment of TIF-2 Deposited 2012-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 299–538（240 aa） Fragment：Ligand Binding Domain, UNP residues 299-538	Not recorded	1PE PENTAETHYLENE GLYCOL × 6 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5.2；298 K；18%-24% PEG 400, 5% glycerol, 0.1M lithium sulfate, and 0.1M sodium acetate pH 5.2, hanging drop vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.238
4IS8 Divergent sequence tunes ligand sensitivity in phospholipid-regulated hormone receptors Deposited 2013-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 300–538（239 aa） Fragment：LIGAND BINDING DOMAIN	Mutation：Q419H,A420T,G421E,A422V,T423A,L424F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG3350, 5% GLYCEROL, 50 MM BIS-TRIS, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.78 Å R-free 0.257
4IS8 Divergent sequence tunes ligand sensitivity in phospholipid-regulated hormone receptors Deposited 2013-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 300–538（239 aa） Fragment：LIGAND BINDING DOMAIN	Mutation：Q419H,A420T,G421E,A422V,T423A,L424F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG3350, 5% GLYCEROL, 50 MM BIS-TRIS, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.78 Å R-free 0.257
4ONI Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids Deposited 2014-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 291–541（251 aa） Fragment：Ligand Binding Domain, UNP residues 291-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；298 K；20-30% PEG 3350, Bis Tris, 5% glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
4ONI Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids Deposited 2014-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 291–541（251 aa） Fragment：Ligand Binding Domain, UNP residues 291-541	Not recorded	P6L (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；298 K；20-30% PEG 3350, Bis Tris, 5% glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
4PLD Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human TIF-2 Deposited 2014-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 301–541（241 aa） Fragment：UNP residues 301-541	Not recorded	CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001	Resolution 1.75 Å R-free 0.225
4PLE Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli Phospholipid and a Fragment of TIF-2 Deposited 2014-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 301–541（241 aa） Fragment：UNP residues 301-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001	Resolution 1.75 Å R-free 0.236
4PLE Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli Phospholipid and a Fragment of TIF-2 Deposited 2014-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 301–541（241 aa） Fragment：UNP residues 301-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001	Resolution 1.75 Å R-free 0.236
4PLE Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli Phospholipid and a Fragment of TIF-2 Deposited 2014-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 301–541（241 aa） Fragment：UNP residues 301-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001	Resolution 1.75 Å R-free 0.236
4PLE Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli Phospholipid and a Fragment of TIF-2 Deposited 2014-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 301–541（241 aa） Fragment：UNP residues 301-541	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001	Resolution 1.75 Å R-free 0.236
5L0M hLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex Deposited 2016-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 79–187（109 aa） Fragment：unp residues 79-187	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M calcium acetate and 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.197
5L11 Human Liver Receptor Homologue-1 (LRH-1) Bound to RJW100 and a Fragment of TIF-2 Deposited 2016-07-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：unp residues 299-541	Not recorded	RJW (1R,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.05 M Sodium Acetate, pH 4.6, PEG 4000 5-11%, glycerol 5-10%	Resolution 1.85 Å R-free 0.241
5SYZ Human Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereoisomer and a Fragment of TIF-2 Deposited 2016-08-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 297–538（242 aa）	Not recorded	71W (1S,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Sodium acetate, PEG4000, glycerol	Resolution 1.93 Å R-free 0.228
5UNJ Structure of Human Liver Receptor Homolog 1 in complex with PGC1a and RJW100 Deposited 2017-01-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：unp residues 299-541	Not recorded	RJW (1R,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.05M Sodium acetate, pH 4.6; PEG4000 14%, glycerol 15-21%	Resolution 1.96 Å R-free 0.227
6OQX Human Liver Receptor Homolog-1 bound to the agonist 5N and a fragment of the Tif2 coregulator Deposited 2019-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：UNP Residues 299-541	Not recorded	N1V (8beta,11alpha,12alpha)-8-(1-phenylethenyl)-1,6:7,14-dicycloprosta-1,3,5,7(14)-tetraen-11-yl sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Sodium acetate (pH 4.6), PEG4000, glycerol	Resolution 2.00 Å R-free 0.245
6OQY Human LRH-1 bound to the agonist 6N and a fragment of the Tif2 coregulator Deposited 2019-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：UNP Residues 299-541	Not recorded	N2J N-[(1S,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-yl]sulfuric diamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Sodium acetate (pH 4.6), PEG4000, glycerol	Resolution 2.23 Å R-free 0.269
6OR1 Human LRH-1 bound to the agonist 2N and a fragment of the Tif2 coregulator Deposited 2019-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：UNP Residues 299-541	Not recorded	N27 N-[(1S,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-yl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.05M sodium acetate (pH 4.6), 5-11% PEG4000, 0-10% glycerol. Microseeding with LRH-1-RJW100 crystals.	Resolution 2.17 Å R-free 0.239
6VC2 LRH-1 bound to SS-RJW100 and a fragment of the Tif2 Coactivator Deposited 2019-12-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa）	Not recorded	QU7 (1S,3aS,6aS)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Sodium acetate, PEG 4000, glycerol	Resolution 1.70 Å R-free 0.228
6VIF Human LRH-1 ligand-binding domain bound to agonist cpd 15 and fragment of coregulator TIF-2 Deposited 2020-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa）	Not recorded	QY4 N-[(8beta,11alpha,12alpha)-8-{[methyl(phenyl)amino]methyl}-1,6:7,14-dicycloprosta-1(6),2,4,7(14)-tetraen-11-yl]sulfuric diamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；Na acetate (pH 4.6), PEG 4000, glycerol	Resolution 2.26 Å R-free 0.284
7JYD Human Liver Receptor Homolog-1 in Complex with 10CA and a Fragment of Tif2 Deposited 2020-08-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：nuclear receptor ligand-binding domain	Not recorded	VQA 10-[(3aR,6R,6aR)-6-hydroxy-3-phenyl-3a-(1-phenylethenyl)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.4 M sodium/potassium tartrate	Resolution 2.30 Å R-free 0.227
7JYE Human Liver Receptor Homolog-1 in Complex with 9ChoP and a Fragment of Tif2 Deposited 2020-08-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：nuclear receptor ligand-binding domain	Not recorded	VQY 9-[(3~{a}~{R},6~{R},6~{a}~{R})-6-oxidanyl-3-phenyl-3~{a}-(1-phenylethenyl)-4,5,6,6~{a}-tetrahydro-1~{H}-pentalen-2-yl]nonyl 2-(trimethyl-$l^{4}-azanyl)ethyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；9-19% tert-butanol, 0-6 % glycerol, 0.1 M tri-sodium citrate pH 4.6	Resolution 2.55 Å R-free 0.187
7TT8 Human LRH-1 LBD bound to agonist 6N-10CA and fragment of Tif2 coactivator Deposited 2022-01-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa）	Not recorded	IUW 10-[(3aR,6S,6aR)-3-phenyl-3a-(1-phenylethenyl)-6-(sulfamoylamino)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；tri-Na citrate (4.6), tert-butanol, glycerol	Resolution 2.80 Å R-free 0.276
8F8M LRH-1 bound to small molecule Tet and fragment of coactivator Tif2 Deposited 2022-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 299–541（243 aa） Fragment：Nuclear receptor ligand-binding domain	Not recorded	XKE (1~{R},3~{a}~{R},6~{a}~{R})-4-phenyl-3~{a}-(1-phenylethenyl)-5-[9-(1~{H}-1,2,3,4-tetrazol-5-yl)nonyl]-2,3,6,6~{a}-tetrahydro-1~{H}-pentalen-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；tri-Na citrate, tert-butanol, glycerol	Resolution 2.60 Å R-free 0.220
8PKI Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Deposited 2023-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain K 39–132（94 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
9SMQ Crystal structure of LRH-1/TIF-2 peptide in complex with CP4 Deposited 2025-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 297–541（245 aa）	Not recorded	A1JOT 3-[5-phenyl-1-[3-(trifluoromethyl)phenyl]pyrazol-3-yl]propanoic acid × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.25 M Ammonium phosphate monobasic 0.9 Ammonium phosphate dibasic	Resolution 2.20 Å R-free 0.244

26 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NR5A2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–249； UniProt 1–248

Nuclear receptor DAX1

OrganismNot specified

UniProt F1D8P4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 140–154	Fragment：UNP residues 140-154	Nuclear receptor subfamily 5 group A member 2 × 1 （O00482） PIZ (2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dihexadecanoate × 1 EDO 1,2-ETHANEDIOL × 5 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；LRH-1/PIP3, 20% PEG 4K, 0.2M NaOAc, 0.1M Tris (8.5), 0.036mM PIP3, 0.90mM 15-mer PRQGSILYSLLTSSK, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.86 Å R-free 0.210

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	F1D8P4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–15； UniProt 140–154

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4rwv
Deposition date deposition_date	2014-12-05
Structure title title	Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution
Keywords keywords	;Ligand-binding domain of nuclear hormone receptor, PF00104 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, Partnership for Stem Cell Biology, TRANSCRIPTION, STEMCELL ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.38 Å
Radius of gyration Rg (electron density) rg_electron	18.81 Å
Forward intensity I(0) i0	16392900.00
Molecular weight molecular_weight	31185.0 kDa
Excluded volume excluded_volume	39413 Å³
Envelope volume envelope_volume	45756 Å³
Hydration-shell volume shell_volume	20250 Å³
Envelope diameter envelope_diameter	66.5 Å
Shell Rg shell_rg	25.32 Å
Envelope Rg envelope_rg	19.09 Å
Shape Rg shape_rg	18.79 Å
Total Rg total_rg	19.84 Å
Total atoms total_atoms	2182
Residues n_residues	257
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.2 Å
Rg (real space) rg_real	20.27 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.6390e+07
I(0) uncertainty (real space) i0_real_error	1.9820e+05
Rg (reciprocal space) rg_reciprocal	20.29 Å
I(0) (reciprocal space) i0_reciprocal	16390000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.326
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2755000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Nuclear receptor subfamily 5 group A member 2
Molecular weight formula_weight	28733.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2494

SQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia Coli

Entity 2 Entity 2 polymer

Description description	Nuclear receptor DAX1
Molecular weight formula_weight	1651.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PRQGSILYSLLTSSK

Entity 3 Entity 3 non-polymer

Description description	;(2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dihexadecanoate ;
Molecular weight formula_weight	1051.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4rwvA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

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8. Citations (1)

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Unit-cell length a length_a	71.616 Å
Unit-cell length b length_b	50.187 Å
Unit-cell length c length_c	93.608 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.859 Å
Low-resolution limit resolution_low	29.463 Å
R factor r_factor	0.1726
R_work r_work	0.1707
R_free r_free	0.2100

fit	/app/data/saxs_computation/rw/4rwv/4rwv.fit
pddf	/app/data/pr_computation/rw/4rwv/4rwv.pr.out
profile	/app/data/saxs_computation/rw/4rwv/4rwv.dat

Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear receptor subfamily 5 group A member 2

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear receptor DAX1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)