8ga8

Structure of the yeast (HDAC) Rpd3L complex

Method: ELECTRON MICROSCOPY D_max: 183.9 Å Quality: GOOD

▼

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

Transcriptional regulatory protein SDS3

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain H； UniProt 1–327	Not recorded	Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

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 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–327（327 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain F 14–324（311 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain F 14–324（311 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	SDS3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–327； UniProt 1–327

Transcriptional regulatory protein SIN3

OrganismNot specified

UniProt P22579

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–1536 Chain D； UniProt 1–1536	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XAW Crystal Structure Analysis of SIN3-UME6 Deposited 2020-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 402–473（72 aa）	Not recorded	BR BROMIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100mM Tris, pH 8.8, 1.36M sodium citrate	Resolution 1.84 Å R-free 0.212
6XDJ Crystal Structure Analysis of MBP-SIN3 Deposited 2020-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 402–473（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris, pH 6.0, 1.6M Ammonium sulfate	Resolution 2.20 Å R-free 0.240
6XDJ Crystal Structure Analysis of MBP-SIN3 Deposited 2020-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 402–473（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris, pH 6.0, 1.6M Ammonium sulfate	Resolution 2.20 Å R-free 0.240
6XDJ Crystal Structure Analysis of MBP-SIN3 Deposited 2020-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 402–473（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris, pH 6.0, 1.6M Ammonium sulfate	Resolution 2.20 Å R-free 0.240
6XDJ Crystal Structure Analysis of MBP-SIN3 Deposited 2020-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 402–473（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris, pH 6.0, 1.6M Ammonium sulfate	Resolution 2.20 Å R-free 0.240
7YI0 Cryo-EM structure of Rpd3S complex Deposited 2022-07-14	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 A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YI2 Cryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex Deposited 2022-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7YI3 Cryo-EM structure of Rpd3S in close-state Rpd3S-NCP complex Deposited 2022-07-14	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 A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–1536（1536 aa） Chain B 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8HXX Cryo-EM structure of the histone deacetylase complex Rpd3S Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8HXY Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain K 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8HY0 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain K 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8IHN Cryo-EM structure of the Rpd3S core complex Deposited 2023-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8IHT Rpd3S bound to the nucleosome Deposited 2023-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain K 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
8JHO Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Deposited 2023-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain K 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å
8KC7 Rpd3S histone deacetylase complex Deposited 2023-08-06	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 B 215–1536（1322 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 2–1536（1535 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 2–1536（1535 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 215–1536（1322 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric	Chain B 2–1536（1535 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 215–1536（1322 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 215–1536（1322 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8TOF Rpd3S bound to an H3K36Cme3 modified nucleosome Deposited 2023-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8W9C Cryo-EM structure of the Rpd3S complex from budding yeast Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain A 1–1536（1536 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain A 662–1344（683 aa） Chain B 662–1344（683 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain A 225–1320（1096 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

28 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SIN3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–1536； UniProt 1–1536 Author chain D； PDBConstruct 1–1536； UniProt 1–1536

Transcriptional regulatory protein SAP30

OrganismNot specified

UniProt P38429

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain J； UniProt 1–201	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–201（201 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain G 71–191（121 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain G 73–191（119 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	SAP30_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–201； UniProt 1–201

Transcriptional regulatory protein PHO23

OrganismNot specified

UniProt P50947

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain L； UniProt 1–330	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain C 1–330（330 aa）	Not recorded	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain I 11–115（105 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain I 11–115（105 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	PHO23_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain L； PDBConstruct 1–330； UniProt 1–330

Transcriptional regulatory protein RXT2

OrganismNot specified

UniProt P38255

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain M； UniProt 1–430	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain E 1–430（430 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain J 157–374（218 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain J 169–374（206 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	RXT2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–430； UniProt 1–430

Transcriptional regulatory protein DEP1

OrganismNot specified

UniProt P31385

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain G； UniProt 1–405	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–405（405 aa）	Not recorded	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain E 177–295（119 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain E 177–295（119 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	DEP1_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–405； UniProt 1–405

Histone deacetylase RPD3

OrganismNot specified

UniProt P32561

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain B； UniProt 1–433 Chain E； UniProt 1–433	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7YI0 Cryo-EM structure of Rpd3S complex Deposited 2022-07-14	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 B 1–433（433 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YI2 Cryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex Deposited 2022-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7YI3 Cryo-EM structure of Rpd3S in close-state Rpd3S-NCP complex Deposited 2022-07-14	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 B 1–433（433 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain F 1–433（433 aa） Chain G 1–433（433 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8HXX Cryo-EM structure of the histone deacetylase complex Rpd3S Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain L 1–433（433 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8HXY Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain L 1–433（433 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8HY0 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain L 1–433（433 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8IHN Cryo-EM structure of the Rpd3S core complex Deposited 2023-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain L 1–433（433 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8IHT Rpd3S bound to the nucleosome Deposited 2023-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain L 1–433（433 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
8JHO Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Deposited 2023-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain L 1–433（433 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å
8KC7 Rpd3S histone deacetylase complex Deposited 2023-08-06	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 A 1–433（433 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–433（433 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–433（433 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–433（433 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric	Chain A 1–433（433 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–433（433 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain A 1–433（433 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8TOF Rpd3S bound to an H3K36Cme3 modified nucleosome Deposited 2023-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8W9C Cryo-EM structure of the Rpd3S complex from budding yeast Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 7 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 7 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 7 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain B 1–433（433 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain C 9–393（385 aa） Chain D 9–393（385 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric	Chain C 9–386（378 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPD3_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain B； PDBConstruct 1–433； UniProt 1–433 Author chain E； PDBConstruct 1–433； UniProt 1–433

Transcriptional regulatory protein RXT3

OrganismNot specified

UniProt Q07458

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain K； UniProt 1–294	Not recorded	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8GA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPO Cryo-EM structure of a SIN3/HDAC complex from budding yeast Deposited 2022-12-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain J 1–294（294 aa）	Not recorded	ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain H 64–274（211 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RXT3_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain K； PDBConstruct 1–294； UniProt 1–294

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ga8
Deposition date deposition_date	2023-02-22
Structure title title	Structure of the yeast (HDAC) Rpd3L complex
Keywords keywords	HDAC, Silencing, chromatin, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	53.64 Å
Radius of gyration Rg (electron density) rg_electron	53.90 Å
Forward intensity I(0) i0	1371480000.00
Molecular weight molecular_weight	312140.0 kDa
Excluded volume excluded_volume	391620 Å³
Envelope volume envelope_volume	583900 Å³
Hydration-shell volume shell_volume	89625 Å³
Envelope diameter envelope_diameter	191.3 Å
Shell Rg shell_rg	56.75 Å
Envelope Rg envelope_rg	53.37 Å
Shape Rg shape_rg	53.92 Å
Total Rg total_rg	53.95 Å
Total atoms total_atoms	22003
Residues n_residues	2675
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	183.9 Å
Rg (real space) rg_real	53.73 Å
Rg uncertainty (real space) rg_real_error	2.17 Å
I(0) (real space) i0_real	1.3710e+09
I(0) uncertainty (real space) i0_real_error	2.7490e+07
Rg (reciprocal space) rg_reciprocal	53.55 Å
I(0) (reciprocal space) i0_reciprocal	1371000000.0000
Solution quality estimate total_estimate	0.8758
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.337
Kurtosis Kurtosis kurtosis	-0.548
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	140500000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.864

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Transcriptional regulatory protein SDS3
Molecular weight formula_weight	37685.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	22011

MAIQKVSNKDLSRKDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRELTGQPPAPFRLRSD

Entity 2 Entity 2 polymer

Description description	Transcriptional regulatory protein SIN3
Molecular weight formula_weight	175047.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKSYNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ

Entity 3 Entity 3 polymer

Description description	Transcriptional regulatory protein SAP30
Molecular weight formula_weight	23064.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MARPVNTNAETESRGRPTQGGGYASNNNGSCNNNNGSNNNNNNNNNNNNNSNNSNNNNGPTSSGRTNGKQRLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQKKKFKMEFRG

Entity 4 Entity 4 polymer

Description description	Transcriptional regulatory protein PHO23
Molecular weight formula_weight	37081.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSSPANLFPGLNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNTEIPRGLRLGVDNHPAMHLHHELMEKIESKSNSKSSQALKSESRREAMAANRRQGEHYSASTHQQDDSKNDANYGGSRHESQDHTGNNTNSRKRANAANTNNADPETKKRKRRVATTAVSPSTISTATAVNNGRIGTSTASRGVSSVGNSNNSRISRPKTNDYGEPLYCYCNQVAYGEMVGCDGADCELEWFHLPCIGLETLPKGKWYCDDCKKKL

Entity 5 Entity 5 polymer

Description description	Transcriptional regulatory protein RXT2
Molecular weight formula_weight	48684.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MTIRSSMKNNAELESKSVLANESNIISTFTRRIIKEKSGNYQVLKRSLDGKLIYPEATGISSNRGNKLLQRSEVVTRRDLNNSKPMIEQTVFYNGSEHRLLQTNIVTDSRRKRIKFTPDINVEPVLVGDENDIDGSEKEDENITDEYYGEEDDDDLSKLVNVKEILTPILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYLGISDDDITIPVALRVVKRGLISATTNKTTNFEEEIENTMEDGVVDDNEPDEEANRA

Entity 6 Entity 6 polymer

Description description	Transcriptional regulatory protein DEP1
Molecular weight formula_weight	47035.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEKSLANLPELKYAPKLSSLVKQETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKSQELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVIPDVNYHVPIKLDNKTLSCITGYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIVDRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDFHQWAQ

Entity 7 Entity 7 polymer

Description description	Histone deacetylase RPD3
Molecular weight formula_weight	48962.0 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY

Entity 8 Entity 8 polymer

Description description	Transcriptional regulatory protein RXT3
Molecular weight formula_weight	33851.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MSVSEQDPNRAYRETQSQIYKLQETLLNSARTKNKQEEGQESNTHSFPEQYMHYQNGRNSAYDLPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDNTLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILVLRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYPSVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQRLDRDKPHEPNGYIKNLKWT

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8ga8B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	8ga8E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	210993

fit	/app/data/saxs_computation/ga/8ga8/8ga8.fit
pddf	/app/data/pr_computation/ga/8ga8/8ga8.pr.out
profile	/app/data/saxs_computation/ga/8ga8/8ga8.dat

Structure of the yeast (HDAC) Rpd3L complex

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

Transcriptional regulatory protein SDS3

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional regulatory protein SIN3

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional regulatory protein SAP30

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional regulatory protein PHO23

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional regulatory protein RXT2

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional regulatory protein DEP1

State in the Current Structure

Other States of the Same Protein in the Database

Histone deacetylase RPD3

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional regulatory protein RXT3

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)