4pc0

Structure of the human RbAp48-MTA1(670-711) complex

Method: X-RAY DIFFRACTION D_max: 106.3 Å Quality: REASONABLE

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

Histone-binding protein RBBP4

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: Dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–425	Not recorded	Metastasis-associated protein MTA1 × 1 （Q13330） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: Dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–425	Not recorded	Metastasis-associated protein MTA1 × 1 （Q13330） 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

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 4PC0	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 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 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 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 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 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
4R7A Crystal Structure of RBBP4 bound to PHF6 peptide Deposited 2014-08-27	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
6NQ3 Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex Deposited 2019-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–425（425 aa）	Not recorded	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
6NQ3 Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex Deposited 2019-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–425（425 aa）	Not recorded	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
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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 1–425； UniProt 1–425 Author chain B； PDBConstruct 1–425； UniProt 1–425

Metastasis-associated protein MTA1

OrganismNot specified

UniProt Q13330

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 C； UniProt 653–694	Fragment：Residues 653-694	Histone-binding protein RBBP4 × 1 （Q09028） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: Dimeric（2） Consistent with protein copy count	Chain D； UniProt 653–694	Fragment：Residues 653-694	Histone-binding protein RBBP4 × 1 （Q09028） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4PC0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BKX The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex Deposited 2013-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 162–335（174 aa） Fragment：ELM2-SANT	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 2 K POTASSIUM ION × 4 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400	Resolution 3.00 Å R-free 0.261
4PBY Structure of the human RbAp48-MTA1(656-686) complex Deposited 2014-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric	Chain C 639–669（31 aa） Fragment：Residues 639-669	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric	Chain D 639–669（31 aa） Fragment：Residues 639-669	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric	Chain B 653–678（26 aa） Fragment：Residues 653-678	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
5FXY Structure of the human RBBP4:MTA1(464-546) complex Deposited 2016-03-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 464–546（83 aa） Fragment：RESIDUES 464-546	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 464–546（83 aa） Fragment：RESIDUES 464-546	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 464–546（83 aa） Fragment：RESIDUES 464-546	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 464–546（83 aa） Fragment：RESIDUES 464-546	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
5ICN HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4 Deposited 2016-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 162–354（193 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400	Resolution 3.30 Å R-free 0.299
6G16 Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange Deposited 2018-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 447–529（83 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 447–529（83 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 447–529（83 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 447–529（83 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
7AO8 Structure of the MTA1/HDAC1/MBD2 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 × 5 PDB declaration: pentameric	Chain A 1–715（715 aa） Chain D 1–715（715 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 4.50 Å
7AO9 Structure of the core MTA1/HDAC1/MBD2 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 × 5 PDB declaration: pentameric	Chain A 1–715（715 aa） Chain D 1–715（715 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 6.10 Å
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 A 1–715（715 aa） Chain D 1–715（715 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

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–42； UniProt 653–694 Author chain D； PDBConstruct 1–42； UniProt 653–694

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4pc0
Deposition date deposition_date	2014-04-14
Structure title title	Structure of the human RbAp48-MTA1(670-711) complex
Keywords keywords	Cell cycle, MTA1-NuRD subcomplex; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	32.95 Å
Radius of gyration Rg (electron density) rg_electron	32.56 Å
Forward intensity I(0) i0	148639000.00
Molecular weight molecular_weight	95370.0 kDa
Excluded volume excluded_volume	118340 Å³
Envelope volume envelope_volume	154980 Å³
Hydration-shell volume shell_volume	40135 Å³
Envelope diameter envelope_diameter	111.5 Å
Shell Rg shell_rg	39.06 Å
Envelope Rg envelope_rg	32.06 Å
Shape Rg shape_rg	32.54 Å
Total Rg total_rg	33.12 Å
Total atoms total_atoms	6734
Residues n_residues	846
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	106.3 Å
Rg (real space) rg_real	32.99 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.4860e+08
I(0) uncertainty (real space) i0_real_error	2.4190e+06
Rg (reciprocal space) rg_reciprocal	32.98 Å
I(0) (reciprocal space) i0_reciprocal	148600000.0000
Solution quality estimate total_estimate	0.6735
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.325
Kurtosis Kurtosis kurtosis	-0.553
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55330000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.968; Smooth: 0.890

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Histone-binding protein RBBP4
Molecular weight formula_weight	47709.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7094

MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Metastasis-associated protein MTA1
Molecular weight formula_weight	4652.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

KLLSSSETKRAARRPYKPIALRQSQALPPRPPPPAPVNDEPI

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	360

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4pc0A00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4pc0B00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	52.250 Å
Unit-cell length b length_b	123.230 Å
Unit-cell length c length_c	87.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2065
R_work r_work	0.2037
R_free r_free	0.2590

fit	/app/data/saxs_computation/pc/4pc0/4pc0.fit
pddf	/app/data/pr_computation/pc/4pc0/4pc0.pr.out
profile	/app/data/saxs_computation/pc/4pc0/4pc0.dat

Structure of the human RbAp48-MTA1(670-711) complex

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

Histone-binding protein RBBP4

State in the Current Structure

Other States of the Same Protein in the Database

Metastasis-associated protein MTA1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)