Polycomb protein EED
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 81–439 | Fragment：UNP residues 81-439 | PALI1 peptide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；3.6 M sodium formate, 10 mM TCEP, 5% glycerol | Resolution 1.63 Å R-free 0.193 |
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 6V3Y | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3IIW Crystal structure of Eed in complex with a trimethylated histone H3K27 peptide Deposited 2009-08-03 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
Fragment：Eed residues 77-441
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；4.0 M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.193 |
| 3IIY Crystal structure of Eed in complex with a trimethylated histone H1K26 peptide Deposited 2009-08-03 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
Fragment：Eed residues 77-441
|
Mutation：M370T | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.65 Å R-free 0.259 |
| 3IJ0 Crystal structure of Eed in complex with a trimethylated histone H3K9 peptide Deposited 2009-08-03 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
Fragment：Eed residues 77-441
|
Mutation：M370T | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.45 Å R-free 0.244 |
| 3IJ1 Crystal structure of Eed in complex with a trimethylated histone H4K20 peptide Deposited 2009-08-03 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
Fragment：Eed residues 77-441
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.204 |
| 3IJC Crystal structure of Eed in complex with NDSB-195 Deposited 2009-08-04 | 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
77–441（365 aa）
Fragment：Eed residues 77-441
|
Mutation：M370T | NDS ETHYL DIMETHYL AMMONIO PROPANE SULFONATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.95 Å R-free 0.232 |
| 3JPX EED: A Novel Histone Trimethyllysine Binder Within The EED-EZH2 Polycomb Complex Deposited 2009-09-04 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
40–441（402 aa）
Fragment：UNP RESIDUE: 40-441
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；300 K；3.5M NaF, 10 mM TCEP Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 2.05 Å R-free 0.211 |
| 3JZG Structure of EED in complex with H3K27me3 Deposited 2009-09-23 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
40–441（402 aa）
Fragment：UNP RESIDUE 40-441
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；300 K；3.5M NaF, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 2.10 Å R-free 0.222 |
| 3JZH EED-H3K79me3 Deposited 2009-09-23 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
40–441（402 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；300 K；3.5M NaF, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 2.05 Å R-free 0.218 |
| 3JZN Structure of EED in apo form Deposited 2009-09-23 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
76–441（366 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；3.5 mM NaF, 10 mM TCEP, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.60 Å R-free 0.239 |
| 3K26 Complex structure of EED and trimethylated H3K4 Deposited 2009-09-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；3.5M NaF, 10 mM TCEP, 15%Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.58 Å R-free 0.197 |
| 3K27 Complex structure of EED and trimethylated H3K9 Deposited 2009-09-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；3.5M NaF, 10 mM TCEP, 15%GLYCEROL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.76 Å R-free 0.198 |
| 4W2R Structure of Hs/AcPRC2 in complex with 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one Deposited 2017-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
81–441（361 aa）
Fragment：UNP residues 81-441
|
Not recorded | ZN ZINC ION × 7 CJD 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.7；286 K；Precipitant: 26.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.70)
|
Resolution 2.81 Å R-free 0.266 |
| 4W2R Structure of Hs/AcPRC2 in complex with 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one Deposited 2017-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
81–441（361 aa）
Fragment：UNP residues 81-441
|
Not recorded | ZN ZINC ION × 7 CJD 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.7；286 K；Precipitant: 26.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.70)
|
Resolution 2.81 Å R-free 0.266 |
| 4X3E Crystal structure of EED in complex with a trimethylated Jarid2 peptide Deposited 2014-11-28 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
Fragment：UNP residues 77-441
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Sodium Formate
|
Resolution 2.30 Å R-free 0.224 |
| 5GSA EED in complex with an allosteric PRC2 inhibitor Deposited 2016-08-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | 73K N-(furan-2-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8；293 K；0.1 M TRIS, 16% PEG 8000
|
Resolution 2.49 Å R-free 0.255 |
| 5GSA EED in complex with an allosteric PRC2 inhibitor Deposited 2016-08-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | 73K N-(furan-2-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8；293 K；0.1 M TRIS, 16% PEG 8000
|
Resolution 2.49 Å R-free 0.255 |
| 5H13 EED in complex with PRC2 allosteric inhibitor EED396 Deposited 2016-10-08 | Different construct 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
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | GOL GLYCEROL × 1 PR PRASEODYMIUM ION × 1 LQA 4-azanylidene-2-(3-methoxy-4-propan-2-yloxy-phenyl)-6,7-dihydro-[1,3]benzodioxolo[6,5-a]quinolizine-3-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；3.3 M Na formate, 0.01 M Yttrium chloride hexahydrate
|
Resolution 1.90 Å R-free 0.229 |
| 5H14 EED in complex with an allosteric PRC2 inhibitor EED666 Deposited 2016-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | GOL GLYCEROL × 1 LQB 2-[3-(3,5-dimethylpyrazol-1-yl)-4-nitro-phenyl]-3,4-dihydro-1H-isoquinoline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 1.90 Å R-free 0.223 |
| 5H14 EED in complex with an allosteric PRC2 inhibitor EED666 Deposited 2016-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | GOL GLYCEROL × 1 LQB 2-[3-(3,5-dimethylpyrazol-1-yl)-4-nitro-phenyl]-3,4-dihydro-1H-isoquinoline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 1.90 Å R-free 0.223 |
| 5H15 EED in complex with PRC2 allosteric inhibitor EED709 Deposited 2016-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQD (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.27 Å R-free 0.236 |
| 5H15 EED in complex with PRC2 allosteric inhibitor EED709 Deposited 2016-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQD (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.27 Å R-free 0.236 |
| 5H17 EED in complex with PRC2 allosteric inhibitor EED210 Deposited 2016-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQE (3R,4aS,10aS)-6-methoxy-3-[(3-methoxyphenyl)methyl]-1-methyl-3,4,4a,5,10,10a-hexahydro-2H-benzo[g]quinoline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000,10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.30 Å R-free 0.239 |
| 5H19 EED in complex with PRC2 allosteric inhibitor EED162 Deposited 2016-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQF 5-(furan-2-ylmethylamino)-9-(phenylmethyl)-8,10-dihydro-7H-[1,2,4]triazolo[3,4-a][2,7]naphthyridine-6-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bis-Tris, 0.2 M MgCl2, 20% PEG 3350
|
Resolution 1.90 Å R-free 0.215 |
| 5H24 EED in complex with PRC2 allosteric inhibitor compound 8 Deposited 2016-10-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQG 5-(furan-2-ylmethylamino)-[1,2,4]triazolo[4,3-a]pyridine-6-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.50 Å R-free 0.255 |
| 5H24 EED in complex with PRC2 allosteric inhibitor compound 8 Deposited 2016-10-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQG 5-(furan-2-ylmethylamino)-[1,2,4]triazolo[4,3-a]pyridine-6-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.50 Å R-free 0.255 |
| 5H25 EED in complex with PRC2 allosteric inhibitor compound 11 Deposited 2016-10-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.88 Å R-free 0.274 |
| 5H25 EED in complex with PRC2 allosteric inhibitor compound 11 Deposited 2016-10-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
|
Resolution 2.88 Å R-free 0.274 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain L
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5HYN Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide Deposited 2016-02-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain R
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG3350, 400mM Ammonian Citrate pH6.5
|
Resolution 2.95 Å R-free 0.273 |
| 5IJ7 Structure of Hs/AcPRC2 in complex with a pyridone inhibitor Deposited 2016-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
81–441（361 aa）
|
Not recorded | 6BN 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one × 1 ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；286 K；24.0 %w/v PEG monomethyl ether 2000,
0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.60)
|
Resolution 2.62 Å R-free 0.238 |
| 5IJ7 Structure of Hs/AcPRC2 in complex with a pyridone inhibitor Deposited 2016-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
81–441（361 aa）
|
Not recorded | 6BN 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one × 1 ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；286 K；24.0 %w/v PEG monomethyl ether 2000,
0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.60)
|
Resolution 2.62 Å R-free 0.238 |
| 5IJ8 Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone inhibitor Deposited 2016-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
81–441（361 aa）
|
Not recorded | 6BN 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one × 1 ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；286 K；24.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M MES (pH 5.80)
|
Resolution 2.99 Å R-free 0.240 |
| 5IJ8 Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone inhibitor Deposited 2016-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
81–441（361 aa）
|
Not recorded | 6BN 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one × 1 ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；286 K；24.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M MES (pH 5.80)
|
Resolution 2.99 Å R-free 0.240 |
| 5K0M Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of EED Deposited 2016-05-17 | Different construct 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
77–441（365 aa）
|
Not recorded | 6PU (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-{4-[4-(methylsulfonyl)piperazin-1-yl]phenyl}pyrrolidin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；290 K；3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5
|
Resolution 1.83 Å R-free 0.185 |
| 5LS6 Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor Deposited 2016-08-22 | 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 B
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 74D 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.67；291 K；24% PEG3350, 400mM Ammonian Citrate pH6.67
|
Resolution 3.47 Å R-free 0.299 |
| 5LS6 Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor Deposited 2016-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 74D 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.67；291 K；24% PEG3350, 400mM Ammonian Citrate pH6.67
|
Resolution 3.47 Å R-free 0.299 |
| 5LS6 Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor Deposited 2016-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 74D 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.67；291 K；24% PEG3350, 400mM Ammonian Citrate pH6.67
|
Resolution 3.47 Å R-free 0.299 |
| 5LS6 Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor Deposited 2016-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain K
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 74D 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.67；291 K；24% PEG3350, 400mM Ammonian Citrate pH6.67
|
Resolution 3.47 Å R-free 0.299 |
| 5TTW Crystal Structure of EED in Complex with UNC4859 Deposited 2016-11-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
|
Not recorded | SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；291.15 K；20% PEG3350, 0.1 M ammonium sulfate, 0.1M Bis Tris pH 5.5
|
Resolution 1.74 Å R-free 0.214 |
| 5TTW Crystal Structure of EED in Complex with UNC4859 Deposited 2016-11-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
76–441（366 aa）
|
Not recorded | SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；291.15 K；20% PEG3350, 0.1 M ammonium sulfate, 0.1M Bis Tris pH 5.5
|
Resolution 1.74 Å R-free 0.214 |
| 5U5H Crystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine Deposited 2016-12-06 | Different construct 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
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | 7VV (6S)-6-[(2-fluoro-5-methoxyphenyl)methyl]-1-(propan-2-yl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 degree Celsius and harvested and soaked in defined drops consisting of 30 uL of precipitant with 1-2 mM of compound (typically solubilized in DMSO) for 24-48 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 3.5 M sodium formate, 1-2 mM of compound, and 30% (v/v) glycerol.
|
Resolution 1.80 Å R-free 0.204 |
| 5U5K Crystal structure of EED in complex with 3-(3-methoxybenzyl)piperidine hydrochloride Deposited 2016-12-06 | Different construct 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
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | FMT FORMIC ACID × 1 7VY (3R)-3-[(3-methoxyphenyl)methyl]piperidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 Celsius and harvested and soaked in defined drops consisting of 30 uL of precipitant with 1-2 mM of compound (typically solubilized in DMSO) for 24-48 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 3.5 M sodium formate, 1-2 mM of compound, and 30% (v/v) glycerol.
|
Resolution 2.33 Å R-free 0.225 |
| 5U5T Crystal structure of EED in complex with H3K27Me3 peptide and 3-(benzo[d][1,3]dioxol-4-ylmethyl)piperidine-1-carboximidamide Deposited 2016-12-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | 7W7 (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Using a PEG/salt combination as a precipitant. Briefly, EED was incubated with 10 mM B-nicotinamide adenine dinucleotide hydrate, 2 mM of a tightly binding proprietary compound, and 0.5 mM of a synthesized peptide which comprises the helix on EZH2 which interacts with EED. The crystals were grown using the vapor diffusion method. One uL of the protein mixture was combined with 1 uL of a precipitant comprised of 20% (w/v) PEG3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5, on a cover slip which was suspended over a reservoir comprised of 0.5 mL of precipitant at 18 Celsius and sealed. The crystals grew in 4-6 days at 18 Celsius and then harvested and soaked in defined drops consisting of 30 uL of precipitant and 2 mM of compound for 24 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 30% PEG 400 (v/v), 20% (w/v) PEG 3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5
|
Resolution 1.60 Å R-free 0.200 |
| 5U5T Crystal structure of EED in complex with H3K27Me3 peptide and 3-(benzo[d][1,3]dioxol-4-ylmethyl)piperidine-1-carboximidamide Deposited 2016-12-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | 7W7 (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide × 1 YT3 YTTRIUM (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Using a PEG/salt combination as a precipitant. Briefly, EED was incubated with 10 mM B-nicotinamide adenine dinucleotide hydrate, 2 mM of a tightly binding proprietary compound, and 0.5 mM of a synthesized peptide which comprises the helix on EZH2 which interacts with EED. The crystals were grown using the vapor diffusion method. One uL of the protein mixture was combined with 1 uL of a precipitant comprised of 20% (w/v) PEG3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5, on a cover slip which was suspended over a reservoir comprised of 0.5 mL of precipitant at 18 Celsius and sealed. The crystals grew in 4-6 days at 18 Celsius and then harvested and soaked in defined drops consisting of 30 uL of precipitant and 2 mM of compound for 24 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 30% PEG 400 (v/v), 20% (w/v) PEG 3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5
|
Resolution 1.60 Å R-free 0.200 |
| 5U62 Crystal structure of EED in complex with H3K27Me3 peptide and 6-(benzo[d][1,3]dioxol-4-ylmethyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine Deposited 2016-12-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | GOL GLYCEROL × 1 YT3 YTTRIUM (III) ION × 2 7WD (6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Using a PEG/salt combination as a precipitant. Briefly, EED was incubated with 10 mM B-nicotinamide adenine dinucleotide hydrate, 2 mM of a tightly binding proprietary compound, and 0.5 mM of a synthesized peptide which comprises the helix on EZH2 which interacts with EED. The crystals were grown using the vapor diffusion method. One uL of the protein mixture was combined with 1 uL of a precipitant comprised of 20% (w/v) PEG3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5, on a cover slip which was suspended over a reservoir comprised of 0.5 mL of precipitant at 18 Celsius and sealed. The crystals grew in 4-6 days at 18 Celsius and then harvested and soaked in defined drops consisting of 30 uL of precipitant and 2 mM of compound for 24 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 30% PEG 400 (v/v), 20% (w/v) PEG 3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5.
|
Resolution 1.90 Å R-free 0.208 |
| 5U62 Crystal structure of EED in complex with H3K27Me3 peptide and 6-(benzo[d][1,3]dioxol-4-ylmethyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine Deposited 2016-12-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
Fragment：UNP residues 76-441
|
Not recorded | 7WD (6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Using a PEG/salt combination as a precipitant. Briefly, EED was incubated with 10 mM B-nicotinamide adenine dinucleotide hydrate, 2 mM of a tightly binding proprietary compound, and 0.5 mM of a synthesized peptide which comprises the helix on EZH2 which interacts with EED. The crystals were grown using the vapor diffusion method. One uL of the protein mixture was combined with 1 uL of a precipitant comprised of 20% (w/v) PEG3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5, on a cover slip which was suspended over a reservoir comprised of 0.5 mL of precipitant at 18 Celsius and sealed. The crystals grew in 4-6 days at 18 Celsius and then harvested and soaked in defined drops consisting of 30 uL of precipitant and 2 mM of compound for 24 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 30% PEG 400 (v/v), 20% (w/v) PEG 3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5.
|
Resolution 1.90 Å R-free 0.208 |
| 5U69 Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine Deposited 2016-12-07 | Different construct 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
77–441（365 aa）
|
Not recorded | LQD (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；290 K；3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5
|
Resolution 1.28 Å R-free 0.152 |
| 5U6D Polycomb protein EED in complex with inhibitor: 2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-fluoro-6-methylphenyl)methyl]pyrrolidin-3-yl}phenyl)-1H-pyrazol-1-yl]acetamide Deposited 2016-12-07 | Different construct 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
77–441（365 aa）
|
Not recorded | 7XG 2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-fluoro-6-methylphenyl)methyl]pyrrolidin-3-yl}phenyl)-1H-pyrazol-1-yl]acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；290 K；3.08M Sodium Formate, 20% Glycerol, 0.1M Tris, pH8.5
|
Resolution 1.64 Å R-free 0.178 |
| 5U8A Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine Deposited 2016-12-14 | Different construct 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
77–441（365 aa）
|
Not recorded | 82D (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；290 K；3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5
|
Resolution 1.45 Å R-free 0.173 |
| 5U8F Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine Deposited 2016-12-14 | Different construct 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
77–441（365 aa）
|
Not recorded | 82G (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；290 K；3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5
|
Resolution 1.34 Å R-free 0.176 |
| 5WG6 Human Polycomb Repressive Complex 2 in complex with GSK126 inhibitor Deposited 2017-07-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–441（440 aa）
|
Not recorded | ZN ZINC ION × 8 A9G 1-[(2S)-butan-2-yl]-N-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；200 mM ammonium citrate pH 7.2, 16% PEG 3350
|
Resolution 3.90 Å R-free 0.300 |
| 5WG6 Human Polycomb Repressive Complex 2 in complex with GSK126 inhibitor Deposited 2017-07-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–441（440 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；200 mM ammonium citrate pH 7.2, 16% PEG 3350
|
Resolution 3.90 Å R-free 0.300 |
| 5WP3 Crystal Structure of EED in complex with EB22 Deposited 2017-08-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
75–441（367 aa）
Fragment：residues 75-401
|
Not recorded | UNX UNKNOWN LIGAND × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG-3350, 0.2 M sodium bromide
|
Resolution 2.55 Å R-free 0.244 |
| 5WUK Crystal structure of EED [G255D] in complex with EZH2 peptide and EED226 compound Deposited 2016-12-19 | 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
76–441（366 aa）
Fragment：UNP residues 76-441
|
Mutation：G255D | GOL GLYCEROL × 1 73K N-(furan-2-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% polyethylene glycol (PEG) 6000, 0.1M Bicine(pH9.0)
|
Resolution 2.03 Å R-free 0.191 |
| 6B3W Structure of Hs/AcPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one Deposited 2017-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
81–441（361 aa）
Fragment：UNP residues 81-441
|
Not recorded | ZN ZINC ION × 7 CJG 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；286 K；23.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M MES (pH 6.20)
|
Resolution 3.05 Å R-free 0.282 |
| 6B3W Structure of Hs/AcPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one Deposited 2017-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
81–441（361 aa）
Fragment：UNP residues 81-441
|
Not recorded | ZN ZINC ION × 7 CJG 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；286 K；23.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M MES (pH 6.20)
|
Resolution 3.05 Å R-free 0.282 |
| 6C23 Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State Deposited 2018-01-05 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain L
1–441（441 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6C24 Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Extended Active State Deposited 2018-01-06 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain L
1–441（441 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6LO2 Crystal structure of EED in complex with EZH2 peptide and compound 11# Deposited 2020-01-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
76–441（366 aa）
|
Not recorded | EJU 8-[4-[(dimethylamino)methyl]phenyl]-N-[(2-methoxyphenyl)methyl]-[1,2,4]triazolo[4,3-a]pyridin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M TRIS pH 8.0, 15.6% PEG 8000
|
Resolution 2.21 Å R-free 0.232 |
| 6LO2 Crystal structure of EED in complex with EZH2 peptide and compound 11# Deposited 2020-01-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
76–441（366 aa）
|
Not recorded | EJU 8-[4-[(dimethylamino)methyl]phenyl]-N-[(2-methoxyphenyl)methyl]-[1,2,4]triazolo[4,3-a]pyridin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M TRIS pH 8.0, 15.6% PEG 8000
|
Resolution 2.21 Å R-free 0.232 |
| 6SFB EED in complex with a triazolopyrimidine Deposited 2019-08-01 | Different construct 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
76–441（366 aa）
|
Not recorded | L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；23% PEG3350, 0.1 M PCTP pH 8.5, 200 mM MgCl2, 10 mM TCEP
|
Resolution 1.52 Å R-free 0.206 |
| 6SFB EED in complex with a triazolopyrimidine Deposited 2019-08-01 | Different construct 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
76–441（366 aa）
|
Not recorded | L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；23% PEG3350, 0.1 M PCTP pH 8.5, 200 mM MgCl2, 10 mM TCEP
|
Resolution 1.52 Å R-free 0.206 |
| 6SFC EED in complex with a methyl-thiazole Deposited 2019-08-01 | Different construct 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
76–441（366 aa）
|
Not recorded | CA CALCIUM ION × 2 L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；23% PEG3350, 0.1 M PCTP pH 8.5, 200 mM MgCl2, 10 mM TCEP
|
Resolution 2.00 Å R-free 0.228 |
| 6SFC EED in complex with a methyl-thiazole Deposited 2019-08-01 | Different construct 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
76–441（366 aa）
|
Not recorded | L9T N-(1,3-benzodioxol-4-ylmethyl)-4-methyl-5-(1-methylpyrazol-3-yl)-1,3-thiazol-2-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；23% PEG3350, 0.1 M PCTP pH 8.5, 200 mM MgCl2, 10 mM TCEP
|
Resolution 2.00 Å R-free 0.228 |
| 6U4Y Crystal Structure of an EZH2-EED Complex in an Oligomeric State Deposited 2019-08-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
78–441（364 aa）
Fragment：UNP residues 78-441
Chain E
78–441（364 aa）
Fragment：UNP residues 78-441
Chain F
78–441（364 aa）
Fragment：UNP residues 78-441
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；1 M sodium/potassium tartrate, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.0
|
Resolution 2.91 Å R-free 0.224 |
| 6V3X Crystal structure of EED in complex with PALI1-K1241me3 peptide Deposited 2019-11-26 | Different construct Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
81–440（360 aa）
Fragment：UNP residues 81-440
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；3.6 M sodium formate, 10 mM TCEP, 5% glycerol
|
Resolution 1.70 Å R-free 0.200 |
| 6W7F Structure of EED bound to inhibitor 5285 Deposited 2020-03-19 | Different construct 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
77–441（365 aa）
|
Not recorded | Q3D 8-(6-cyclopropylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 4.3 M Sodium Formate, 18% Glycerol, 10 mM TCEP
|
Resolution 2.20 Å R-free 0.199 |
| 6W7G Structure of EED bound to inhibitor 1056 Deposited 2020-03-19 | Different construct 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
77–441（365 aa）
|
Not recorded | Q3A 8-(2,6-dimethylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine × 3 NA SODIUM ION × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 4.2 M Sodium Formate, 18% glycerol, 10 mM TCEP
|
Resolution 1.85 Å R-free 0.191 |
| 6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric |
Chain L
1–441（441 aa）
|
Not recorded | MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6YVI EED in complex with a cyano-benzofuran Deposited 2020-04-28 | Different construct 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
76–441（366 aa）
|
Not recorded | CA CALCIUM ION × 1 L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.15M CaCl2, 18% PEG 3350, 0.1M PCPT pH 8.3
|
Resolution 2.26 Å R-free 0.241 |
| 6YVI EED in complex with a cyano-benzofuran Deposited 2020-04-28 | Different construct 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
76–441（366 aa）
|
Not recorded | PV5 5-fluoranyl-4-[[[8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-yl]amino]methyl]-2,3-dihydro-1-benzofuran-7-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.15M CaCl2, 18% PEG 3350, 0.1M PCPT pH 8.3
|
Resolution 2.26 Å R-free 0.241 |
| 6YVJ EED in complex with a triazolopyrimidine Deposited 2020-04-28 | Different construct 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
76–441（366 aa）
|
Not recorded | L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 1.84 Å R-free 0.199 |
| 6YVJ EED in complex with a triazolopyrimidine Deposited 2020-04-28 | Different construct 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
76–441（366 aa）
|
Not recorded | GOL GLYCEROL × 1 EJR N-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 1.84 Å R-free 0.199 |
| 7KSO Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 Deposited 2020-11-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7KSR PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome Deposited 2020-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7KTP PRC2:EZH1_B from a dimeric PRC2 bound to a nucleosome Deposited 2020-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 7KXT Crystal structure of human EED Deposited 2020-12-04 | Different construct 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
40–441（402 aa）
|
Not recorded | XB7 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine × 1 UNX UNKNOWN LIGAND × 27 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；3.5M Sodium Formate, 0.1M TrisCl pH8.5
|
Resolution 2.15 Å R-free 0.215 |
| 7KXT Crystal structure of human EED Deposited 2020-12-04 | Different construct 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
40–441（402 aa）
|
Not recorded | XB7 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine × 1 UNX UNKNOWN LIGAND × 25 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；3.5M Sodium Formate, 0.1M TrisCl pH8.5
|
Resolution 2.15 Å R-free 0.215 |
| 7MSB Structure of EED bound to EEDi-4259 Deposited 2021-05-11 | Different construct 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
77–441（365 aa）
|
Not recorded | ZNG (9aM,12aS)-12-{[(5-fluoro-1-benzofuran-4-yl)methyl]amino}-7-(trifluoromethyl)-4,5-dihydro-3H-2,4,11,12a-tetraazabenzo[4,5]cycloocta[1,2,3-cd]inden-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；2uL of protein + 2 uL of well (0.1 M Tris pH 8.5, 20% glycerol, 4.3 M Na Formate, 10 mM TCEP)
|
Resolution 1.90 Å R-free 0.190 |
| 7MSD Structure of EED bound to EEDi-6068 Deposited 2021-05-11 | Different construct 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
77–441（365 aa）
|
Not recorded | ZMY (9aP,12aR)-4-(2,2-difluoropropyl)-12-{[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]amino}-7-(trifluoromethyl)-4,5-dihydro-3H-2,4,8,11,12a-pentaazabenzo[4,5]cycloocta[1,2,3-cd]inden-3-one × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 20% glycerol, 4.5 M Na Formate, 10 mM TCEP
|
Resolution 2.20 Å R-free 0.212 |
| 7P3C EED in complex with compound 4 Deposited 2021-07-07 | Different construct 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
76–441（366 aa）
|
Not recorded | L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 1.61 Å R-free 0.206 |
| 7P3C EED in complex with compound 4 Deposited 2021-07-07 | Different construct 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
76–441（366 aa）
|
Not recorded | 51A N-[5-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methylamino]-[1,2,4]triazolo[4,3-c]pyrimidin-8-yl]benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 1.61 Å R-free 0.206 |
| 7P3G EED in complex with compound 4 Deposited 2021-07-07 | Different construct 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
76–441（366 aa）
|
Not recorded | L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 2.39 Å R-free 0.239 |
| 7P3G EED in complex with compound 4 Deposited 2021-07-07 | Different construct 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
76–441（366 aa）
|
Not recorded | 52R N5-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-N8-methyl-N8-(1-methylpyrazol-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidine-5,8-diamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 2.39 Å R-free 0.239 |
| 7P3J EED in complex with compound 4 Deposited 2021-07-07 | Different construct 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
76–441（366 aa）
|
Not recorded | MG MAGNESIUM ION × 3 L9W N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 1.93 Å R-free 0.204 |
| 7P3J EED in complex with compound 4 Deposited 2021-07-07 | Different construct 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
76–441（366 aa）
|
Not recorded | 54N 8-[6-[(dimethylamino)methyl]-2-methyl-pyridin-3-yl]-5-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methylamino]-2H-pyrido[3,4-d]pyridazin-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2
|
Resolution 1.93 Å R-free 0.204 |
| 7QJG EED in complex with PRC2 allosteric inhibitor compound 6 Deposited 2021-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
|
Not recorded | CL CHLORIDE ION × 2 EKR N-(2,3-dihydro-1-benzofuran-7-ylmethyl)-8-[4-[(dimethylamino)methyl]phenyl]-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.0, 16% PEG 8000
|
Resolution 1.80 Å R-free 0.218 |
| 7QJG EED in complex with PRC2 allosteric inhibitor compound 6 Deposited 2021-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
77–441（365 aa）
|
Not recorded | CL CHLORIDE ION × 2 EKR N-(2,3-dihydro-1-benzofuran-7-ylmethyl)-8-[4-[(dimethylamino)methyl]phenyl]-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.0, 16% PEG 8000
|
Resolution 1.80 Å R-free 0.218 |
| 7QJU EED in complex with PRC2 allosteric inhibitor compound 7 Deposited 2021-12-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
|
Not recorded | CL CHLORIDE ION × 2 EKF N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-[4-[(dimethylamino)methyl]phenyl]-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.0, 16% PEG 8000
|
Resolution 1.80 Å R-free 0.213 |
| 7QJU EED in complex with PRC2 allosteric inhibitor compound 7 Deposited 2021-12-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
77–441（365 aa）
|
Not recorded | CL CHLORIDE ION × 2 EKF N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-[4-[(dimethylamino)methyl]phenyl]-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.0, 16% PEG 8000
|
Resolution 1.80 Å R-free 0.213 |
| 7QK4 EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683) Deposited 2021-12-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–441（365 aa）
|
Not recorded | CL CHLORIDE ION × 3 EJR N-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M MgCl2, 20% PEG 3350
|
Resolution 1.60 Å R-free 0.206 |
| 7SI4 CRYSTAL STRUCTURE OF EED WITH MRTX-2219 Deposited 2021-10-12 | Different construct 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
40–441（402 aa）
|
Not recorded | 9JL (4S)-8-{4-[(dimethylamino)methyl]-2-methylphenyl}-5-{[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]amino}imidazo[1,2-c]pyrimidine-2-carbonitrile × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；3.5 M Sodium Formate, 50 mM 0.1 M Hepes pH 7.0
|
Resolution 1.90 Å R-free 0.213 |
| 7SI5 CRYSTAL STRUCTURE OF EED WITH MRTX-1919 Deposited 2021-10-12 | Different construct 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
40–441（402 aa）
|
Not recorded | NA SODIUM ION × 2 9L0 (4R)-8-(1,3-dimethyl-1H-pyrazol-5-yl)-5-{[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]amino}imidazo[1,2-c]pyrimidine-2-carbonitrile × 1 EDO 1,2-ETHANEDIOL × 2 FMT FORMIC ACID × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；3.1 mM Sodium Formate, 100 mM Hepes pH 7.5, seeding
|
Resolution 1.75 Å R-free 0.187 |
| 7TD5 Structure of human PRC2-EZH1 containing phosphorylated SUZ12 Deposited 2021-12-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；10% PEG3350, 100 mM (NH4)2SO4, 50mM HEPES 6.8
|
Resolution 2.99 Å R-free 0.230 |
| 7TD5 Structure of human PRC2-EZH1 containing phosphorylated SUZ12 Deposited 2021-12-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
77–441（365 aa）
|
Not recorded | ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；10% PEG3350, 100 mM (NH4)2SO4, 50mM HEPES 6.8
|
Resolution 2.99 Å R-free 0.230 |
| 8EQV Cryo-EM structure of PRC2 in complex with the long isoform of AEBP2 Deposited 2022-10-09 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
1–441（441 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；200 mM NaCl, 20 mM HEPES pH 7.5, 1 mM TCEP, 0.01% NP-40
cryo-EM vitrification conditions
Cryogen ETHANE；Blotting 3 seconds
|
Resolution 3.64 Å |
| 8FYH G4 RNA-mediated PRC2 dimer Deposited 2023-01-26 | 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 × 12 PDB declaration: tridecameric |
Chain C
1–441（441 aa）
Chain I
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1mM TCEP)
EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1mM TCEP)
EM preparation buffer II (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, 0.01%NP-40, and 1mM TCEP).
cryo-EM vitrification conditions
Cryogen ETHANE；3s of single side blotting
|
Resolution 3.40 Å |
| 8T9G Automethylated PRC2 dimer bound to nucleosome Deposited 2023-06-23 | 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 × 19 PDB declaration: 21-meric |
Chain F
1–441（441 aa）
Chain K
1–441（441 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.20 Å |
| 8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain G
1–441（441 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8TB9 PRC2-J119-450 monomer bound to H1-nucleosome Deposited 2023-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric |
Chain G
1–441（441 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8VMI PRC2_AJ119-450 bound to H3K4me3 Deposited 2024-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VML PRC2_AJ1-450 bound to H3K4me3 Deposited 2024-01-13 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain L
1–441（441 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8VNV PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged Deposited 2024-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain L
1–441（441 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VNZ PRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H3 tail disengaged Deposited 2024-01-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain L
1–441（441 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9C8U Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min Deposited 2024-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
75–441（367 aa）
|
Not recorded | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9DCH Single-stranded RNA-mediated PRC2 dimer Deposited 2024-08-26 | 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 × 12 PDB declaration: tridecameric |
Chain C
1–441（441 aa）
Chain J
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1 mM TCEP)
EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1 mM TCEP)
EM preparation buffer II (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, 0.01%NP-40, and 1 mM TCEP).
cryo-EM vitrification conditions
Cryogen ETHANE；2-3s of single side blotting
|
Resolution 3.40 Å |
77 other PDB entries and 112 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | EED_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–359； UniProt 81–439 |
