8d8i

Crystal structure of Reverb alpha in complex with synthetic agonist

Method: X-RAY DIFFRACTION D_max: 59.8 Å Quality: REASONABLE

▼

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

Nuclear receptor subfamily 1 group D member 1

Homo sapiens

UniProt P20393

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 281–323 Chain A； UniProt 425–614	Not recorded	Nuclear receptor corepressor 1 × 1 （O75376） QFX (4S)-6-[([1,1'-biphenyl]-2-yl)oxy]-3-chloro[1,2,4]triazolo[4,3-b]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；80mM Na Hepes pH7.5, 200mM proline, 8% glycerol and 18% PEG3350	Resolution 2.50 Å R-free 0.239

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 8D8I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A6Y REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX Deposited 1998-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 123–216（94 aa） Fragment：DNA BINDING DOMAIN CONSISTS OF RESIDUES A 101 TO A 164, B 101 TO B 164 Chain B 123–216（94 aa） Fragment：DNA BINDING DOMAIN CONSISTS OF RESIDUES A 101 TO A 164, B 101 TO B 164	Mutation：H116L Mutation：H116L	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；PROTEIN AND DNA COMPLEX WAS CRYSTALLIZED FROM 25-30% PEG 8000, 5 MM MGCL2, 400 MM NACL2, 100 MM TRIS, PH 7.5., VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.288
1GA5 CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT Deposited 2000-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION Chain B 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG8000, 5mM MgCl2, 400 mM NaCl, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.40 Å R-free 0.299
1GA5 CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT Deposited 2000-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain E 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION Chain F 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG8000, 5mM MgCl2, 400 mM NaCl, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.40 Å R-free 0.299
1HLZ CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT Deposited 2000-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION Chain B 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG8000, 5 mM MgCl2, 400 mM NaCl, Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.80 Å R-free 0.310
3N00 Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A Deposited 2010-05-13	Different construct 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 281–323（43 aa） Chain A 423–614（192 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.60 Å R-free 0.266
3N00 Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A Deposited 2010-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 281–323（43 aa） Chain A 423–614（192 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.60 Å R-free 0.266

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NR1D1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–47； UniProt 281–323 Author chain A； PDBConstruct 48–237； UniProt 425–614

Nuclear receptor corepressor 1

Homo sapiens

UniProt O75376

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 2045–2064	Mutation：C2056A	Nuclear receptor subfamily 1 group D member 1 × 1 （P20393） QFX (4S)-6-[([1,1'-biphenyl]-2-yl)oxy]-3-chloro[1,2,4]triazolo[4,3-b]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；80mM Na Hepes pH7.5, 200mM proline, 8% glycerol and 18% PEG3350	Resolution 2.50 Å R-free 0.239

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8D8I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EQR Solution structure of the first SANT domain from human nuclear receptor corepressor 1 Deposited 2007-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 433–486（54 aa） Fragment：Sant domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.14mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3H52 Crystal structure of the antagonist form of human glucocorticoid receptor Deposited 2009-04-21	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 N 2258–2276（19 aa） Fragment：CORNR box 3, UNP residues 2258-2276	Not recorded	486 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP	Resolution 2.80 Å R-free 0.283
3H52 Crystal structure of the antagonist form of human glucocorticoid receptor Deposited 2009-04-21	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 M 2258–2276（19 aa） Fragment：CORNR box 3, UNP residues 2258-2276	Not recorded	486 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP	Resolution 2.80 Å R-free 0.283
3KMZ Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment Deposited 2009-11-11	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 C 2047–2065（19 aa） Fragment：NR1 Chain D 2047–2065（19 aa） Fragment：NR1	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EQO 4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid × 2 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；18% PEG 3350 (w/v), 0.15M NH4Cl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.230
3KMZ Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment Deposited 2009-11-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2047–2065（19 aa） Fragment：NR1	Non-standard monomer：Yes (specific site not provided by mmCIF)	EQO 4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid × 2 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；18% PEG 3350 (w/v), 0.15M NH4Cl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.230
3KMZ Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment Deposited 2009-11-11	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 D 2047–2065（19 aa） Fragment：NR1	Non-standard monomer：Yes (specific site not provided by mmCIF)	EQO 4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid × 2 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；18% PEG 3350 (w/v), 0.15M NH4Cl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.230
3N00 Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A Deposited 2010-05-13	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 B 2045–2065（21 aa） Fragment：CORNR box 2 residues 2045-2065	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.60 Å R-free 0.266
3N00 Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A Deposited 2010-05-13	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 2045–2065（21 aa） Fragment：CORNR box 2 residues 2045-2065	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.60 Å R-free 0.266
4MDD Crystal Structure of the Glucocorticoid Receptor Bound to a Non-steroidal Antagonist Reveals Repositioning and Partial Disordering of Activation Function Helix 12 Deposited 2013-08-22	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 C 2260–2274（15 aa） Fragment：unp residues 2260-2274 Chain D 2260–2274（15 aa） Fragment：unp residues 2260-2274	Not recorded	29M N-[2-{[benzyl(methyl)amino]methyl}-3-(4-fluoro-2-methoxyphenyl)-5-(propan-2-yl)-1H-indol-7-yl]methanesulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；100mM Tris HCl plus 6% 1,6 - Hexanediol + 24% PEG 8K, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.40 Å R-free 0.258
4WVD Identification of a novel FXR ligand that regulates metabolism Deposited 2014-11-05	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 C 2259–2275（17 aa） Fragment：UNP residues 2259-2275	Not recorded	FMT FORMIC ACID × 4 IVM (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；50mM HEPES pH7.0, 3.5M sodium formate	Resolution 2.90 Å R-free 0.302
4WVD Identification of a novel FXR ligand that regulates metabolism Deposited 2014-11-05	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 D 2259–2275（17 aa） Fragment：UNP residues 2259-2275	Not recorded	FMT FORMIC ACID × 4 IVM (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；50mM HEPES pH7.0, 3.5M sodium formate	Resolution 2.90 Å R-free 0.302
6WMQ Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID1 Peptide Deposited 2020-04-21	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 E 2044–2066（23 aa） Chain F 2044–2066（23 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；2.0 M ammonium sulfate, 0.1 M Na HEPES, pH 7.5, 2% PEG 400	Resolution 2.55 Å R-free 0.270
6XXS Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide. Deposited 2020-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1340–1356（17 aa） Chain D 1340–1356（17 aa） Chain G 1340–1356（17 aa） Chain H 1340–1356（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2M Sodium chloride 5%(w/v) PEG 4000 0.1M Tris base/ Hydrochloric acid pH 8.5	Resolution 3.25 Å R-free 0.225
6XYX Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide Deposited 2020-01-31	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 C 1340–1356（17 aa） Chain D 1340–1356（17 aa）	Not recorded	NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Sodium acetate trihydrate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350	Resolution 1.44 Å R-free 0.198
6XZZ Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD2 peptide Deposited 2020-02-05	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 B 1726–1742（17 aa）	Not recorded	NA SODIUM ION × 14 CL CHLORIDE ION × 4 TFA trifluoroacetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；13.4%(v/v) PEG 400, 0.335M K2HPO4 / NaH2PO4 pH 7.5	Resolution 1.39 Å R-free 0.206
6Y17 Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with nebulinSH3-NCoR1BBD1 Deposited 2020-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1733–1741（9 aa） Chain B 1733–1741（9 aa） Chain C 1340–1356（17 aa） Chain D 1340–1356（17 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.66 M ammonium sulfate, 3.3% (v/v) glycerol, 0.05 M magnesium sulfate, 0.1 M imidazole/ hydrochloric acid pH 6.5	Resolution 1.56 Å R-free 0.201
6ZBU Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide Deposited 2020-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1733–1741（9 aa） Chain B 1733–1741（9 aa） Chain C 1340–1356（17 aa） Chain D 1340–1356（17 aa） Chain E 1733–1741（9 aa） Chain F 1733–1741（9 aa） Chain G 1340–1356（17 aa） Chain H 1340–1356（17 aa） Chain I 1733–1741（9 aa） Chain J 1733–1741（9 aa） Chain K 1340–1356（17 aa） Chain L 1340–1356（17 aa）	Not recorded	SO4 SULFATE ION × 28 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.34M Ammonium sulfate 0.67%(v/v) MPD 0.1M HEPES/ Sodium hydroxide pH 7.5	Resolution 2.46 Å R-free 0.259
8AS9 Crystal structure of the talin-KANK1 complex Deposited 2022-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 1341–1356（16 aa）	Not recorded	SO4 SULFATE ION × 12 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；1M Ammonium sulfate, 0.1M CHES 9.5, 0.2M Sodium chloride, 6 % (v/v) Glycerol	Resolution 3.40 Å R-free 0.285
8DKN PPARg bound to T0070907 and Co-R peptide Deposited 2022-07-05	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 C 2260–2272（13 aa）	Not recorded	EEY 2-chloro-5-nitro-N-(pyridin-4-yl)benzamide × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；296 K；2+2 uL drops made from a 2:2:1 molar ratio of T007:NCOR peptide:PPARg and well solution containing 1.8-2.2 M (NH3)2SO4, 0.2 M Li2SO4 and 100 mM CAPS pH 9.5. Protein formulated at 20 mg mL-1 in 20 mM Tris, pH 8.0, 100 mM NaCl, and 1mM TCEP	Resolution 1.95 Å R-free 0.297
8DKV PPARg bound to JTP-426467 and Co-R peptide Deposited 2022-07-06	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 C 2259–2272（14 aa）	Not recorded	SKL 2-chloro-N-[4-(5-methyl-1,3-benzoxazol-2-yl)phenyl]-5-nitrobenzamide × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；2+2 uL drops made from a 2:2:1 molar ratio of JTP-4:NCOR peptide:PPARg and well solution containing 1.8-2.2 M (NH3)2SO4, 0.2 M Li2SO4 and 100 mM CAPS pH 9.5. Protein formulated at 20 mg mL-1 in 20 mM Tris, pH 8.0, 100 mM NaCl, and 1mM TCEP	Resolution 1.59 Å R-free 0.266
8FHE Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and GW9662 Deposited 2022-12-14	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 D 2256–2278（23 aa）	Not recorded	GW9 2-chloro-5-nitro-N-phenylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 1.80 Å R-free 0.229
8FHG Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and ZINC5672437 Deposited 2022-12-14	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 D 2256–2278（23 aa）	Not recorded	XZK N-(4-carbamoylphenyl)-2-chloro-5-nitrobenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 1.80 Å R-free 0.234
8FKC Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33544 Deposited 2022-12-21	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 D 2256–2278（23 aa）	Not recorded	Y5F 2-chloro-N-(5-cyanopyridin-3-yl)-5-nitrobenzamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 1.42 Å R-free 0.198
8FKD Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33068 Deposited 2022-12-21	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 D 2256–2278（23 aa）	Not recorded	Y5O 2-chloro-N-(6-cyanopyridin-3-yl)-5-nitrobenzamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 2.22 Å R-free 0.251
8FKE Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR32904 Deposited 2022-12-21	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 D 2256–2278（23 aa）	Not recorded	Y5T 2-chloro-N-(2-methylpyridin-4-yl)-5-nitrobenzamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 2.02 Å R-free 0.249
8FKF Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR36706 Deposited 2022-12-21	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 D 2256–2278（23 aa）	Not recorded	Y5X 2-chloro-N-(5-fluoropyridin-3-yl)-5-nitrobenzamide × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 1.82 Å R-free 0.216
8FKG Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33486 Deposited 2022-12-21	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 D 2256–2278（23 aa）	Not recorded	GOL GLYCEROL × 2 Y62 2-chloro-N-(5-cyanopyridin-2-yl)-5-nitrobenzamide × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 8 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000	Resolution 2.12 Å R-free 0.218
9O9N Crystal structure of PPARgamma ligand binding domain (LBD) in complex with NCoR1 corepressor peptide and inverse agonist FX-909 Deposited 2025-04-18	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 D 2256–2278（23 aa）	Not recorded	A1CAA (3P)-3-(5,7-difluoro-4-oxo-1,4-dihydroquinolin-2-yl)-4-(methanesulfonyl)benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES (pH 6.5), 0.2 M Ammonium Sulfate, 30% PEG 8000	Resolution 2.10 Å R-free 0.297
9OLC Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746 Deposited 2025-05-12	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 F 2260–2272（13 aa）	Not recorded	A1CCT (3P)-4-chloro-3-(5,7-difluoro-4-oxo-1,4-dihydroquinolin-2-yl)benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M MES pH 6.5, 0.1M Ammonium Sulfate, 24% PEG8000	Resolution 2.83 Å R-free 0.298
9OLC Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746 Deposited 2025-05-12	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 E 2260–2272（13 aa）	Not recorded	A1CCT (3P)-4-chloro-3-(5,7-difluoro-4-oxo-1,4-dihydroquinolin-2-yl)benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M MES pH 6.5, 0.1M Ammonium Sulfate, 24% PEG8000	Resolution 2.83 Å R-free 0.298
9OLC Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746 Deposited 2025-05-12	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 G 2260–2272（13 aa）	Not recorded	A1CCT (3P)-4-chloro-3-(5,7-difluoro-4-oxo-1,4-dihydroquinolin-2-yl)benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M MES pH 6.5, 0.1M Ammonium Sulfate, 24% PEG8000	Resolution 2.83 Å R-free 0.298
9OLC Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746 Deposited 2025-05-12	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 H 2260–2272（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M MES pH 6.5, 0.1M Ammonium Sulfate, 24% PEG8000	Resolution 2.83 Å R-free 0.298

24 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCOR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–20； UniProt 2045–2064

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8d8i
Deposition date deposition_date	2022-06-08
Structure title title	Crystal structure of Reverb alpha in complex with synthetic agonist
Keywords keywords	REV-ERB, Nuclear receptor, Agonist, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	18.81 Å
Radius of gyration Rg (electron density) rg_electron	17.51 Å
Forward intensity I(0) i0	11173400.00
Molecular weight molecular_weight	25362.0 kDa
Excluded volume excluded_volume	32008 Å³
Envelope volume envelope_volume	36198 Å³
Hydration-shell volume shell_volume	17430 Å³
Envelope diameter envelope_diameter	63.3 Å
Shell Rg shell_rg	23.56 Å
Envelope Rg envelope_rg	17.77 Å
Shape Rg shape_rg	17.48 Å
Total Rg total_rg	18.55 Å
Total atoms total_atoms	1795
Residues n_residues	221
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

▼

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

Maximum dimension Dmax dmax	59.8 Å
Rg (real space) rg_real	18.71 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.1170e+07
I(0) uncertainty (real space) i0_real_error	1.5840e+05
Rg (reciprocal space) rg_reciprocal	18.73 Å
I(0) (reciprocal space) i0_reciprocal	11170000.0000
Solution quality estimate total_estimate	0.6524
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.324
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2115000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 0.999; Sysdev: 0.313; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nuclear receptor subfamily 1 group D member 1
Molecular weight formula_weight	26490.2 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	1821

GSHMPEPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFRVDAQ

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Nuclear receptor corepressor 1
Molecular weight formula_weight	2280.6 kDa
Mutation mutation	C2056A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

THRLITLADHIAQIITQDFA

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 3 Entity 3 non-polymer

Description description	(4S)-6-[([1,1'-biphenyl]-2-yl)oxy]-3-chloro[1,2,4]triazolo[4,3-b]pyridazine
Molecular weight formula_weight	322.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

▶

8. Citations (1)

▶

Unit-cell length a length_a	115.073 Å
Unit-cell length b length_b	115.073 Å
Unit-cell length c length_c	107.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.504 Å
Low-resolution limit resolution_low	73.030 Å
R factor r_factor	0.2069
R_work r_work	0.2052
R_free r_free	0.2395

fit	/app/data/saxs_computation/d8/8d8i/8d8i.fit
pddf	/app/data/pr_computation/d8/8d8i/8d8i.pr.out
profile	/app/data/saxs_computation/d8/8d8i/8d8i.dat

Crystal structure of Reverb alpha in complex with synthetic agonist

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

Nuclear receptor subfamily 1 group D member 1

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear receptor corepressor 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)