6cht

HNF4alpha in complex with the corepressor EBP1 fragment

Method: X-RAY DIFFRACTION D_max: 195.9 Å Quality: GOOD

▼

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

Hepatocyte nuclear factor 4-alpha

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 178–421 Chain B； UniProt 178–421 Chain J； UniProt 178–421 Chain K； UniProt 178–421 Chain M； UniProt 178–421 Chain N； UniProt 178–421 Chain V； UniProt 178–421 Chain W； UniProt 178–421	Not recorded	Proliferation-associated protein 2G4 × 2 （Q9UQ80） DAO LAURIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol	Resolution 3.17 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain D； UniProt 178–421 Chain E； UniProt 178–421 Chain G； UniProt 178–421 Chain H； UniProt 178–421 Chain P； UniProt 178–421 Chain Q； UniProt 178–421 Chain S； UniProt 178–421 Chain T； UniProt 178–421	Not recorded	Proliferation-associated protein 2G4 × 2 （Q9UQ80） DAO LAURIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol	Resolution 3.17 Å R-free 0.274

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 6CHT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PZL Crystal structure of HNF4a LBD in complex with the ligand and the coactivator SRC-1 peptide Deposited 2003-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 133–369（237 aa） Fragment：HNF4A-LDB	Mutation：D137L, S138A	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Sodium, Potassium Tartrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.10 Å R-free 0.267
3CBB Crystal Structure of Hepatocyte Nuclear Factor 4alpha in complex with DNA: Diabetes Gene Product Deposited 2008-02-21	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 58–135（78 aa） Fragment：DNA binding domain Chain B 58–135（78 aa） Fragment：DNA binding domain	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；26% PEG 4000, 80mM Magnesium acetate, 50mM Sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.252
3FS1 Crystal structure of HNF4a LBD in complex with the ligand and the coactivator PGC-1a fragment Deposited 2009-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 148–377（230 aa） Fragment：HNF4a Ligand Binding Domain	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.236
4B7W Ligand binding domain human hepatocyte nuclear factor 4alpha: Apo form Deposited 2012-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377 Chain B 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377 Chain C 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377 Chain D 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.7 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, 10 MM DTT, 16% MPD IN 0.1 M TRIS, PH 8.0	Resolution 4.00 Å R-free 0.280
4IQR Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA Deposited 2013-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 55–377（323 aa） Fragment：unp residues 55-377 Chain B 55–377（323 aa） Fragment：unp residues 55-377	Not recorded	MYR MYRISTIC ACID × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M MES, 25mM NH4Cl, 25mM MgCl2 and PEG 3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.278
4IQR Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA Deposited 2013-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain E 55–377（323 aa） Fragment：unp residues 55-377 Chain F 55–377（323 aa） Fragment：unp residues 55-377	Not recorded	MYR MYRISTIC ACID × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M MES, 25mM NH4Cl, 25mM MgCl2 and PEG 3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.278
8C1L Crystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide Deposited 2022-12-20	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 148–377（230 aa） Chain B 148–377（230 aa）	Not recorded	PLM PALMITIC ACID × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；284 K；20% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 8.5 -- 0.2M sodium nitrate	Resolution 2.00 Å R-free 0.237
9IBR Crystal structure of HNF4 alpha LBD complexed with GRIP-1 peptide and ESY13 Deposited 2025-02-13	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 A 148–377（230 aa）	Not recorded	A1I1W 2-hydroxy-5-(phenylethynyl)benzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；16% PEG3350 8% ethylene glycol 0.1M bis-tris-propane pH 8.5 -	Resolution 2.78 Å R-free 0.355

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HNF4A_HUMAN
Isoform	P41235-4
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–245； UniProt 178–421 Author chain B； PDBConstruct 2–245； UniProt 178–421 Author chain D； PDBConstruct 2–245； UniProt 178–421 Author chain E； PDBConstruct 2–245； UniProt 178–421 Author chain G； PDBConstruct 2–245； UniProt 178–421 Author chain H； PDBConstruct 2–245； UniProt 178–421 Author chain J； PDBConstruct 2–245； UniProt 178–421 Author chain K； PDBConstruct 2–245； UniProt 178–421 Author chain M； PDBConstruct 2–245； UniProt 178–421 Author chain N； PDBConstruct 2–245； UniProt 178–421 Author chain P； PDBConstruct 2–245； UniProt 178–421 Author chain Q； PDBConstruct 2–245； UniProt 178–421 Author chain S； PDBConstruct 2–245； UniProt 178–421 Author chain T； PDBConstruct 2–245； UniProt 178–421 Author chain V； PDBConstruct 2–245； UniProt 178–421 Author chain W； PDBConstruct 2–245； UniProt 178–421

Proliferation-associated protein 2G4

OrganismNot specified

UniProt Q9UQ80

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain C； UniProt 349–368 Chain L； UniProt 349–368	Not recorded	Hepatocyte nuclear factor 4-alpha × 8 （P41235） DAO LAURIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol	Resolution 3.17 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain F； UniProt 349–368 Chain I； UniProt 349–368	Not recorded	Hepatocyte nuclear factor 4-alpha × 8 （P41235） DAO LAURIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol	Resolution 3.17 Å R-free 0.274

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6CHT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Q8K The crystal structure of Ebp1 Deposited 2007-06-11	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 2–394（393 aa）	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；2.3 M Ammoniumsulfate, 0.1M Citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.219
3J2I Structure of late pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel Deposited 2012-10-04	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 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1.5 mM or 5 mM MgCl2, 0.075% (v/v) NP-40 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2 seconds before plunging in liquid ethane (FEI VITROBOT MARK IV)	Resolution 11.90 Å
6LSR Cryo-EM structure of a pre-60S ribosomal subunit - state B Deposited 2020-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain z 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 246	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
6SXO Cryo-EM structure of the human Ebp1-ribosome complex Deposited 2019-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6WM8 Proliferation-Associated protein 2G4 (PA2G4) Deposited 2020-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–362（361 aa） Chain B 2–362（361 aa） Chain C 2–362（361 aa）	Not recorded	SO4 SULFATE ION × 28	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.4M Ammonium Sulphate 100 sodium citrate pH 5.0	Resolution 2.60 Å R-free 0.238
6Z6L Cryo-EM structure of human CCDC124 bound to 80S ribosomes Deposited 2020-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6Z6M Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 Deposited 2020-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6Z6N Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1) Deposited 2020-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6ZM7 SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex Deposited 2020-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6ZME SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex Deposited 2020-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 83 PDB declaration: 88-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6ZMI SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex Deposited 2020-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
6ZMO SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex Deposited 2020-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 256 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7BHP Cryo-EM structure of the human Ebp1 - 80S ribosome Deposited 2021-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 45-meric	Chain A 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 41 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8K2C Cryo-EM structure of the human 80S ribosome with Tigecycline Deposited 2023-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 259 T1C TIGECYCLINE × 9 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
8XSX Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2 Deposited 2024-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 259 T1C TIGECYCLINE × 7 ZN ZINC ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
8XSY Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled) Deposited 2024-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 255 T1C TIGECYCLINE × 8 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8XSZ Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNA Deposited 2024-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric	Chain CA 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 248 T1C TIGECYCLINE × 5 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B0P In situ human Hibernating class1 80S ribosome Deposited 2024-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 255 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9FQZ CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 Deposited 2024-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain CA 1–394（394 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 271 K POTASSIUM ION × 104 ZN ZINC ION × 8 PUT 1,4-DIAMINOBUTANE × 7 HYG HYGROMYCIN B × 1 SPD SPERMIDINE × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ANM ANISOMYCIN × 1 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
9GJ5 Human 80S ribosome in complex with NatA in distal position and Ebp1 Deposited 2024-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain A 1–394（394 aa）	Not recorded	KGN D-chiro inositol hexakisphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.61 Å
9P78 In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9P79 In situ human Hibernating rotate3 with Z site tRNA state 80S ribosome Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9P7A In situ human hibernating class2 80S ribosome Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9P7C In situ human Hibernating class3 80S ribosome Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9P7D In situ human Hibernating class4 80S ribosome Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
9P7E In situ human Hibernating class5 80S ribosome Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9P8C In situ human Hibernating class1 (rotate3) without E tRNA state 80S ribosome Deposited 2025-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
9P9J In situ human 60S ribosome Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 191 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9P9K In situ human 60S ribosome with EIF6 Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 191 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9PA7 In situ human 80S consensus ribosome with EBP1 Deposited 2025-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric	Chain CA 7–362（356 aa）	Not recorded	MG MAGNESIUM ION × 225 SPM SPERMINE × 8 SPD SPERMIDINE × 12 K POTASSIUM ION × 75 ZN ZINC ION × 7 PUT 1,4-DIAMINOBUTANE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA2G4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 349–368 Author chain F； PDBConstruct 1–20； UniProt 349–368 Author chain I； PDBConstruct 1–20； UniProt 349–368 Author chain L； PDBConstruct 1–20； UniProt 349–368

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	6cht
Deposition date deposition_date	2018-02-22
Structure title title	HNF4alpha in complex with the corepressor EBP1 fragment
Keywords keywords	;HNF4alpha, EBP1, nuclear receptor, co-repressor, protein-protein interaction, gene regulation, insulin secretion, diabetes, 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	56.83 Å
Radius of gyration Rg (electron density) rg_electron	56.68 Å
Forward intensity I(0) i0	1770090000.00
Molecular weight molecular_weight	374540.0 kDa
Excluded volume excluded_volume	478340 Å³
Envelope volume envelope_volume	707500 Å³
Hydration-shell volume shell_volume	104440 Å³
Envelope diameter envelope_diameter	197.7 Å
Shell Rg shell_rg	58.28 Å
Envelope Rg envelope_rg	55.52 Å
Shape Rg shape_rg	56.72 Å
Total Rg total_rg	56.55 Å
Total atoms total_atoms	26337
Residues n_residues	3261
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	195.9 Å
Rg (real space) rg_real	56.99 Å
Rg uncertainty (real space) rg_real_error	1.77 Å
I(0) (real space) i0_real	1.7700e+09
I(0) uncertainty (real space) i0_real_error	3.3430e+07
Rg (reciprocal space) rg_reciprocal	56.66 Å
I(0) (reciprocal space) i0_reciprocal	1769000000.0000
Solution quality estimate total_estimate	0.8480
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.0 Å
Skewness Skewness skewness	0.410
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	255000000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.793

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Hepatocyte nuclear factor 4-alpha
Molecular weight formula_weight	27535.9 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,G,H,J,K,M,N,P,Q,S,T,V,W
Atom count atom_count	26381

GSLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGSPSDAPHAHHPLHP

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	Proliferation-associated protein 2G4
Molecular weight formula_weight	2205.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

VQDAELKALLQSSASRKTQK

Entity 3 Entity 3 non-polymer

Description description	LAURIC ACID
Molecular weight formula_weight	200.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

▼

7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	6chtA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtJ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtK00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtM00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtN00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtP00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtQ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtS00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtT00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtV00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6chtW00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

▶

8. Citations (1)

▶

Unit-cell length a length_a	139.721 Å
Unit-cell length b length_b	104.946 Å
Unit-cell length c length_c	139.563 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.174 Å
Low-resolution limit resolution_low	49.632 Å
R factor r_factor	0.4142
R_work r_work	0.2622
R_free r_free	0.2742

fit	/app/data/saxs_computation/ch/6cht/6cht.fit
pddf	/app/data/pr_computation/ch/6cht/6cht.pr.out
profile	/app/data/saxs_computation/ch/6cht/6cht.dat

HNF4alpha in complex with the corepressor EBP1 fragment

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

Hepatocyte nuclear factor 4-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Proliferation-associated protein 2G4

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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)