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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q12432 New Search
23PDB entries
24Biological assembly
43chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2K3X Solution structure of EAF3 chromo barrel domain Deposited 2008-05-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–113（113 aa） Fragment：UNP residues 1 to 113
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.4-1.5 mM [U-100% 15N] Eaf3, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 800 mM urea, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.4-1.5 mM [U-100% 13C; U-100% 15N] Eaf3, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 800 mM urea, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2K3Y Solution structure of EAF3 chromo barrel domain bound to histone h3 with a dimethyllysine analog H3K36ME2 Deposited 2008-05-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–115（115 aa） Fragment：UNP residues 1 to 115
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.4-1.5 mM [U-100% 15N] entity, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.4-1.5 mM [U-100% 13C; U-100% 15N] entity, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
3E9F Crystal structure short-form (residue1-113) of Eaf3 chromo domain Deposited 2008-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–113（113 aa） Fragment：Eaf3, UNP residues 1-113
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；30% polyethylene glycol 6000, 0.1M MES, pH 6.0, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Resolution 1.80 Å R-free 0.217
3E9G Crystal structure long-form (residue1-124) of Eaf3 chromo domain Deposited 2008-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–124（124 aa） Fragment：Eaf3, UNP residues 1-124
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；2.4M ammonium sulfate, 4% acetone, 0.1 MBicine, pH 9.0, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.267
3E9G Crystal structure long-form (residue1-124) of Eaf3 chromo domain Deposited 2008-08-22 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–124（124 aa） Fragment：Eaf3, UNP residues 1-124
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；2.4M ammonium sulfate, 4% acetone, 0.1 MBicine, pH 9.0, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.267
6K5W Solution structure of the chromodomain of yeast Eaf3 Deposited 2019-05-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–120（120 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 30；Pressure 1
NMR sample composition 1.47 mM [U-13C,15N] Eaf3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.47 mM [U-13C,15N] Eaf3, 100% D2O | 100% D2O
NMR sample composition 1.47 mM [U-15N] Eaf3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7YI0 Cryo-EM structure of Rpd3S complex Deposited 2022-07-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain C 1–401（401 aa）
Chain E 1–401（401 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
7YI1 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Deposited 2022-07-14 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–401（401 aa）
Chain L 1–401（401 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7YI2 Cryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex Deposited 2022-07-14 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers
Chain C 1–401（401 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain C 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain C 1–401（401 aa）
Chain E 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain C 1–401（401 aa）
Chain E 1–401（401 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
8KC7 Rpd3S histone deacetylase complex Deposited 2023-08-06 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–401（401 aa）
Chain F 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers
Chain D 1–401（401 aa）
Chain E 1–401（401 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain C 1–401（401 aa）
Chain D 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers
Chain C 1–401（401 aa）
Chain D 1–401（401 aa）
Chain G 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers
Chain C 1–401（401 aa）
Chain D 1–401（401 aa）
Chain G 1–401（401 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 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers
Chain C 1–401（401 aa）
Chain D 1–401（401 aa）
Chain G 1–401（401 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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.