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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：Q04779 New Search
17PDB entries
17Biological assembly
34chain/assembly records
Main Difference Dimensions in This Set
Different mutation/modification Different assembly state Different ligand/ion 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
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 D 1–684（684 aa）
Chain F 1–684（684 aa）
Mutation：F567A 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 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers
Chain D 1–684（684 aa）
Chain E 1–684（684 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 D 1–684（684 aa）
Chain E 1–684（684 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 D 1–684（684 aa）
Chain F 1–684（684 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 D 1–684（684 aa）
Chain F 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain G 1–684（684 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 F 1–684（684 aa）
Chain G 1–684（684 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 E 1–684（684 aa）
Chain F 1–684（684 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 E 1–684（684 aa）
Chain F 1–684（684 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 E 1–684（684 aa）
Chain F 1–684（684 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 E 1–684（684 aa）
Chain F 1–684（684 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.