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6nq3

Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex

Method: X-RAY DIFFRACTION Dmax: 158.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-binding protein RBBP4

Homo sapiens

UniProt Q09028

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–425 Not recorded Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 1–425 Not recorded Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230

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 6NQ3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2XU7 Structural basis for RbAp48 binding to FOG-1 Deposited 2010-10-15 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 1–425（425 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% (W/V) PEG 3350, 0.2 M NA-MALONATE PH 7.0
Resolution 1.90 Å R-free 0.225
2XU7 Structural basis for RbAp48 binding to FOG-1 Deposited 2010-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% (W/V) PEG 3350, 0.2 M NA-MALONATE PH 7.0
Resolution 1.90 Å R-free 0.225
3GFC Crystal Structure of Histone-binding protein RBBP4 Deposited 2009-02-26 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 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25% PEG3350, 0.2M MgCl2, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.261
4PBY Structure of the human RbAp48-MTA1(656-686) complex Deposited 2014-04-14 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 1–425（425 aa）
Not recorded IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；10% w/v PEG 20000, 20% v/v PEGMME 550, 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, and 0.1 M MES/imidazole pH 6.5
Resolution 2.50 Å R-free 0.225
4PBY Structure of the human RbAp48-MTA1(656-686) complex Deposited 2014-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric
Chain B 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；10% w/v PEG 20000, 20% v/v PEGMME 550, 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, and 0.1 M MES/imidazole pH 6.5
Resolution 2.50 Å R-free 0.225
4PBZ Structure of the human RbAp48-MTA1(670-695) complex Deposited 2014-04-14 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 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v 2-Methyl-2,4-pentanediol (MPD), 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, and 0.1 M MES/imidazole pH 6.5.
Resolution 2.15 Å R-free 0.231
4PC0 Structure of the human RbAp48-MTA1(670-711) complex Deposited 2014-04-14 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 1–425（425 aa）
Not recorded GOL GLYCEROL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M calcium acetate and 20% w/v PEG 3350
Resolution 2.50 Å R-free 0.259
4PC0 Structure of the human RbAp48-MTA1(670-711) complex Deposited 2014-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric
Chain B 1–425（425 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M calcium acetate and 20% w/v PEG 3350
Resolution 2.50 Å R-free 0.259
4R7A Crystal Structure of RBBP4 bound to PHF6 peptide Deposited 2014-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M potassium thiocyanate,30% PEGMME2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.85 Å R-free 0.207
5FXY Structure of the human RBBP4:MTA1(464-546) complex Deposited 2016-03-03 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 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.21 M AMMONIUM CITRATE AND 19% PEG 3350, pH 7.5
Resolution 3.20 Å R-free 0.291
5FXY Structure of the human RBBP4:MTA1(464-546) complex Deposited 2016-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.21 M AMMONIUM CITRATE AND 19% PEG 3350, pH 7.5
Resolution 3.20 Å R-free 0.291
5FXY Structure of the human RBBP4:MTA1(464-546) complex Deposited 2016-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.21 M AMMONIUM CITRATE AND 19% PEG 3350, pH 7.5
Resolution 3.20 Å R-free 0.291
5FXY Structure of the human RBBP4:MTA1(464-546) complex Deposited 2016-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.21 M AMMONIUM CITRATE AND 19% PEG 3350, pH 7.5
Resolution 3.20 Å R-free 0.291
5VTB Crystal structure of RBBP4 bound to BCL11a peptide Deposited 2017-05-16 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 1–425（425 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG2000 MME, 0.1 M potassium thiocyanate
Resolution 2.40 Å R-free 0.244
5WAI Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex Deposited 2017-06-26 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 1–425（425 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG6000, 5%v/v(+/-)-2-Methyl-2,4-pentaneediol (MPD) and 100mM HEPES pH 7.5
Resolution 2.90 Å R-free 0.216
5WAI Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex Deposited 2017-06-26 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 1–425（425 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG6000, 5%v/v(+/-)-2-Methyl-2,4-pentaneediol (MPD) and 100mM HEPES pH 7.5
Resolution 2.90 Å R-free 0.216
5WAK Crystal Structure of a Suz12-Rbbp4 Binary Complex Deposited 2017-06-26 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 1–425（425 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 100 mM ammonium citrate tribasic and 100 mM Tris-HCl, pH 8.6
Resolution 3.20 Å R-free 0.251
5XWR Crystal Structure of RBBP4-peptide complex Deposited 2017-06-30 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 1–425（425 aa）
Chain B 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M Bis-Tris, pH5.5, 25% PEG 3,350
Resolution 2.69 Å R-free 0.256
5XXQ Crystal structure of RBBP4: ZNF827 and its function in telomere Deposited 2017-07-04 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 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；283 K；0.2M Ammonium sulfate, 0.1M MES monohydrate pH 6.5 , 30%(w/v) Polyethylene glycol monomethyl ether 5,000
Resolution 1.90 Å R-free 0.212
5XXQ Crystal structure of RBBP4: ZNF827 and its function in telomere Deposited 2017-07-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；283 K；0.2M Ammonium sulfate, 0.1M MES monohydrate pH 6.5 , 30%(w/v) Polyethylene glycol monomethyl ether 5,000
Resolution 1.90 Å R-free 0.212
5Y1U Crystal structure of RBBP4 bound to AEBP2 RRK motif Deposited 2017-07-21 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 1–425（425 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；283 K；0.2M Ammonium sulfate, 0.1M MES monohydrate pH 6.5 , 30%(w/v) Polyethylene glycol monomethyl ether 5,000
Resolution 2.14 Å R-free 0.219
5Y1U Crystal structure of RBBP4 bound to AEBP2 RRK motif Deposited 2017-07-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；283 K；0.2M Ammonium sulfate, 0.1M MES monohydrate pH 6.5 , 30%(w/v) Polyethylene glycol monomethyl ether 5,000
Resolution 2.14 Å R-free 0.219
6BW3 Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide Deposited 2017-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–425（425 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；20% PEG3350, 0.2 M sodium malonate, 0.1 M BisTris
Resolution 2.20 Å R-free 0.246
6BW3 Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide Deposited 2017-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–425（425 aa）
Not recorded UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；20% PEG3350, 0.2 M sodium malonate, 0.1 M BisTris
Resolution 2.20 Å R-free 0.246
6BW4 Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide Deposited 2017-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；22% PEG3350, 0.2 M Sodium malonate, 0.1 M BisTris
Resolution 2.00 Å R-free 0.233
6BW4 Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide Deposited 2017-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–425（425 aa）
Not recorded UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；22% PEG3350, 0.2 M Sodium malonate, 0.1 M BisTris
Resolution 2.00 Å R-free 0.233
6C23 Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State Deposited 2018-01-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain N 1–425（425 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain N 1–425（425 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
6G16 Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange Deposited 2018-03-20 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 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.21 M AMMONIUM CITRATE, 19% PEG 3350, 15 mM MALTOSE pH 7.5
Resolution 2.80 Å R-free 0.263
6G16 Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange Deposited 2018-03-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.21 M AMMONIUM CITRATE, 19% PEG 3350, 15 mM MALTOSE pH 7.5
Resolution 2.80 Å R-free 0.263
6G16 Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange Deposited 2018-03-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.21 M AMMONIUM CITRATE, 19% PEG 3350, 15 mM MALTOSE pH 7.5
Resolution 2.80 Å R-free 0.263
6G16 Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange Deposited 2018-03-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.21 M AMMONIUM CITRATE, 19% PEG 3350, 15 mM MALTOSE pH 7.5
Resolution 2.80 Å R-free 0.263
6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 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 N 1–425（425 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
6ZRC Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines Deposited 2020-07-13 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 1–425（425 aa）
Not recorded PXY PARA-XYLENE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；20% PEG3350 0.15M DL-malic acid pH 7.1
Resolution 2.60 Å R-free 0.293
6ZRC Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines Deposited 2020-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded PXY PARA-XYLENE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；20% PEG3350 0.15M DL-malic acid pH 7.1
Resolution 2.60 Å R-free 0.293
6ZRD STRUCTURE OF THE HUMAN RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines Deposited 2020-07-13 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 1–425（425 aa）
Not recorded SEZ 1,3,5-trimethylbenzene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG3350 0.2M ammonium acetate 0.1M Bis-TRIS pH 5.5
Resolution 2.50 Å R-free 0.282
6ZRD STRUCTURE OF THE HUMAN RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines Deposited 2020-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded SEZ 1,3,5-trimethylbenzene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG3350 0.2M ammonium acetate 0.1M Bis-TRIS pH 5.5
Resolution 2.50 Å R-free 0.282
7AOA Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex Deposited 2020-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–425（425 aa）
Chain G 1–425（425 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10
Resolution 19.40 Å
7KSO Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 Deposited 2020-11-23 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 D 1–425（425 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 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 D 1–425（425 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 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 D 1–425（425 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
7M40 Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4) Deposited 2021-03-19 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 1–425（425 aa）
Not recorded YQJ N~3~-{4-[3-(dimethylamino)pyrrolidin-1-yl]-6,7-dimethoxyquinazolin-2-yl}-N~1~,N~1~-dimethylpropane-1,3-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；23% PEG3350, 0.2N ammonium acetate, 0.1M Bis-tris pH5.5
Resolution 1.88 Å R-free 0.236
7M40 Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4) Deposited 2021-03-19 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 1–425（425 aa）
Not recorded YQJ N~3~-{4-[3-(dimethylamino)pyrrolidin-1-yl]-6,7-dimethoxyquinazolin-2-yl}-N~1~,N~1~-dimethylpropane-1,3-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；23% PEG3350, 0.2N ammonium acetate, 0.1M Bis-tris pH5.5
Resolution 1.88 Å R-free 0.236
7N40 Crystal structure of LIN9-RbAp48-LIN37, a MuvB subcomplex Deposited 2021-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Bis-Tris, pH 6.5, 20% PEG3350, 0.2 M sodium tartrate
Resolution 2.55 Å R-free 0.249
7R1D Structure of MuvB complex Deposited 2022-02-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–425（425 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7Y5K Crystal structure of human CAF-1 core complex in spacegroup C2221 Deposited 2022-06-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–425（425 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate
Resolution 3.48 Å R-free 0.257
7Y5L Crystal structure of human CAF-1 core complex in spacegroup C2 Deposited 2022-06-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate
Resolution 3.42 Å R-free 0.237
7Y5L Crystal structure of human CAF-1 core complex in spacegroup C2 Deposited 2022-06-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–425（425 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate
Resolution 3.42 Å R-free 0.237
7Y5O Crystal structure of human CAF-1 core complex in spacegroup P21 Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–425（425 aa）
Chain F 1–425（425 aa）
Not recorded GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate
Resolution 3.57 Å R-free 0.232
7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–425（425 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y5V Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 1–425（425 aa）
Chain H 1–425（425 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
8EQV Cryo-EM structure of PRC2 in complex with the long isoform of AEBP2 Deposited 2022-10-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–425（425 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 D 1–425（425 aa）
Chain J 1–425（425 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
8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 1–425（425 aa）
Chain H 1–425（425 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8IQG Cryo-EM structure of the monomeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–425（425 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 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 L 1–425（425 aa）
Chain O 1–425（425 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 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 O 1–425（425 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 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 O 1–425（425 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
8TX8 Crystal Structure of RBBP4 bound to ZNF512B peptide Deposited 2023-08-22 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 1–425（425 aa）
Not recorded FMT FORMIC ACID × 3 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Condition Morpheus G2 0.1 M MES/imidazole, pH 6.5, 40% v/v ethylene glycol; 20 % w/v PEG 8000, 0.1 M mixture of carboxylic acids
Resolution 2.20 Å R-free 0.244
8TX8 Crystal Structure of RBBP4 bound to ZNF512B peptide Deposited 2023-08-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–425（425 aa）
Not recorded FMT FORMIC ACID × 3 EDO 1,2-ETHANEDIOL × 4 ACT ACETATE ION × 1 OXM OXAMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Condition Morpheus G2 0.1 M MES/imidazole, pH 6.5, 40% v/v ethylene glycol; 20 % w/v PEG 8000, 0.1 M mixture of carboxylic acids
Resolution 2.20 Å R-free 0.244
8VMI PRC2_AJ119-450 bound to H3K4me3 Deposited 2024-01-13 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 N 1–425（425 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–425（425 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 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 N 1–425（425 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 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 N 1–425（425 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 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 D 1–425（425 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 D 1–425（425 aa）
Chain K 1–425（425 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
9V5M The crystal structure of RBBP4-H3 complex Deposited 2025-05-26 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 1–425（425 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.211
9XZI Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex Deposited 2025-08-27 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–425（425 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Sodium Citrate, Sodium Acetate, PEG 4000
Resolution 2.69 Å R-free 0.253

49 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBBP4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 15–439； UniProt 1–425 Author chain E； PDBConstruct 15–439； UniProt 1–425

Polycomb protein SUZ12

Homo sapiens

UniProt Q15022

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 76–545 Not recorded Histone-binding protein RBBP4 × 2 （Q09028） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain F； UniProt 76–545 Not recorded Histone-binding protein RBBP4 × 2 （Q09028） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230

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 6NQ3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 T 545–725（181 aa）
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 S 545–725（181 aa）
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
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 C 558–685（128 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 H 558–685（128 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 M 558–685（128 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 S 558–685（128 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 C 558–685（128 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 H 558–685（128 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 M 558–685（128 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 S 558–685（128 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 S 545–725（181 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 T 545–725（181 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain T 545–725（181 aa）
Mutation：Y641N 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 545–725（181 aa）
Mutation：Y641N 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
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 C 558–685（128 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 F 558–685（128 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 I 558–685（128 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 L 558–685（128 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
5WAI Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex Deposited 2017-06-26 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 76–545（470 aa） Fragment：UNP residues 76-545
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG6000, 5%v/v(+/-)-2-Methyl-2,4-pentaneediol (MPD) and 100mM HEPES pH 7.5
Resolution 2.90 Å R-free 0.216
5WAI Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex Deposited 2017-06-26 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 F 76–545（470 aa） Fragment：UNP residues 76-545
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG6000, 5%v/v(+/-)-2-Methyl-2,4-pentaneediol (MPD) and 100mM HEPES pH 7.5
Resolution 2.90 Å R-free 0.216
5WAK Crystal Structure of a Suz12-Rbbp4 Binary Complex Deposited 2017-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 76–545（470 aa） Fragment：UNP residues 76-545
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 100 mM ammonium citrate tribasic and 100 mM Tris-HCl, pH 8.6
Resolution 3.20 Å R-free 0.251
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 A 543–695（153 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 C 543–695（153 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
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 T 545–725（181 aa）
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 S 545–725（181 aa）
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–739（739 aa）
Chain M 1–739（739 aa）
Chain Q 1–739（739 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–739（739 aa）
Chain M 1–739（739 aa）
Chain Q 1–739（739 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
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 A 1–739（739 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
7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–739（739 aa）
Not recorded ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
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 C 1–739（739 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 C 1–739（739 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 C 1–739（739 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
7TD5 Structure of human PRC2-EZH1 containing phosphorylated SUZ12 Deposited 2021-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 561–739（179 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 561–739（179 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–739（739 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 B 1–739（739 aa）
Chain H 1–739（739 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 B 68–685（618 aa）
Chain G 68–685（618 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 D 68–685（618 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 D 68–685（618 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 mutation/modification 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 L 1–739（739 aa）
Chain T 1–739（739 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–739（739 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 A 68–685（618 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 A 1–739（739 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 B 1–739（739 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 B 1–739（739 aa）
Chain I 1–739（739 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
9XZI Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex Deposited 2025-08-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 76–545（470 aa） Fragment：residues 76-545
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Sodium Citrate, Sodium Acetate, PEG 4000
Resolution 2.69 Å R-free 0.253

29 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUZ12_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–470； UniProt 76–545 Author chain F； PDBConstruct 1–470； UniProt 76–545

PHD finger protein 19

Homo sapiens

UniProt Q5T6S3

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 500–580 Not recorded Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） Protein Jumonji × 2 （Q92833） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain G； UniProt 500–580 Not recorded Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） Protein Jumonji × 2 （Q92833） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230

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 6NQ3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4BD3 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity Deposited 2012-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–95（58 aa） Fragment：TUDOR DOMAIN, RESIDUES 38-95
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0
NMR sample composition 90% WATER/10% D2O
Resolution not provided
6WAU Complex structure of PHF19 Deposited 2020-03-26 Different construct 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 38–96（59 aa）
Not recorded UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Resolution 1.75 Å R-free 0.250
6WAU Complex structure of PHF19 Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 38–96（59 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Resolution 1.75 Å R-free 0.250
6WAU Complex structure of PHF19 Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 38–96（59 aa）
Not recorded UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Resolution 1.75 Å R-free 0.250
6WAU Complex structure of PHF19 Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 38–96（59 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Resolution 1.75 Å R-free 0.250
6WAU Complex structure of PHF19 Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 38–96（59 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Resolution 1.75 Å R-free 0.250
6WAU Complex structure of PHF19 Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 38–96（59 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Resolution 1.75 Å R-free 0.250
9XZI Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex Deposited 2025-08-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 531–580（50 aa） Fragment：residues 531-580
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Sodium Citrate, Sodium Acetate, PEG 4000
Resolution 2.69 Å R-free 0.253

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

View Construct and Data Evidence
UniProt name PHF19_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 4–84； UniProt 500–580 Author chain G； PDBConstruct 4–84； UniProt 500–580

Protein Jumonji

OrganismNot specified

UniProt Q92833

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain D； UniProt 147–165 Not recorded Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain H； UniProt 147–165 Not recorded Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0 Resolution 2.89 Å R-free 0.230

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 6NQ3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C23 Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State Deposited 2018-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 68–412（345 aa）
Chain E 68–412（345 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 68–412（345 aa）
Chain E 68–412（345 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 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 × 17 PDB declaration: octadecameric
Chain B 1–450（450 aa）
Chain E 1–450（450 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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
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 F 1–1246（1246 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
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 B 119–450（332 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 F 1–1246（1246 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–1246（1246 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 mutation/modification 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 B 2–450（449 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 mutation/modification 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 2–450（449 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 E 139–169（31 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 E 119–450（332 aa）
Chain L 119–450（332 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

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name JARD2_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–19； UniProt 147–165 Author chain H； PDBConstruct 1–19； UniProt 147–165

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

SAXS profile for 6nq3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6nq3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6nq3
Deposition date deposition_date2019-01-19
Structure title titleCrystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex
Keywords keywordsMethyltransferase, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.89 Å
Radius of gyration Rg (electron density) rg_electron44.23 Å
Forward intensity I(0) i0427258000.00
Molecular weight molecular_weight169210.0 kDa
Excluded volume excluded_volume211630 ų
Envelope volume envelope_volume306310 ų
Hydration-shell volume shell_volume59287 ų
Envelope diameter envelope_diameter176.1 Å
Shell Rg shell_rg46.53 Å
Envelope Rg envelope_rg45.14 Å
Shape Rg shape_rg44.21 Å
Total Rg total_rg44.40 Å
Total atoms total_atoms11928
Residues n_residues1470
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax158.4 Å
Rg (real space) rg_real44.17 Å
Rg uncertainty (real space) rg_real_error1.67 Å
I(0) (real space) i0_real4.2730e+08
I(0) uncertainty (real space) i0_real_error8.6060e+06
Rg (reciprocal space) rg_reciprocal43.89 Å
I(0) (reciprocal space) i0_reciprocal427100000.0000
Solution quality estimate total_estimate0.8276
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.4 Å
Skewness Skewness skewness0.529
Kurtosis Kurtosis kurtosis-0.004
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57820000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.865; Smooth: 0.658
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6nq3A00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6nq3E00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)