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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：P25694 New Search
22PDB entries
22Biological assembly
128chain/assembly records
Main Difference Dimensions in This Set
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
6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
Resolution 3.90 Å
6OAA Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1 Deposited 2019-03-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
Resolution 4.10 Å
6OAB Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2 Deposited 2019-03-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 10 BEF BERYLLIUM TRIFLUORIDE ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
Resolution 3.60 Å
6OMB Cdc48 Hexamer (Subunits A to E) with substrate bound to the central pore Deposited 2019-04-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 10 BEF BERYLLIUM TRIFLUORIDE ION × 8 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6OPC Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) Deposited 2019-04-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 10 BEF BERYLLIUM TRIFLUORIDE ION × 8 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8DAR Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP Deposited 2022-06-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging
Resolution 3.00 Å
8DAS Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA) Deposited 2022-06-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging
Resolution 3.50 Å
8DAT Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB) Deposited 2022-06-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging
Resolution 3.80 Å
8DAU Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) Deposited 2022-06-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging
Resolution 3.70 Å
8DAV Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uC) Deposited 2022-06-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging
Resolution 3.50 Å
8DAW Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) Deposited 2022-06-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging
Resolution 3.60 Å
8U7T Substrate-bound Cdc48, Class 1 Deposited 2023-09-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 8 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8U8I Cdc48-Shp1 unfolding native substrate, Class 4 Deposited 2023-09-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 8 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8U9C Cdc48-Shp1 unfolding native substrate, Class 5 Deposited 2023-09-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 8 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U9P Cdc48-Shp1 unfolding native substrate, Class 2 Deposited 2023-09-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 8 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8U9Q Cdc48-Shp1 unfolding native substrate, Class 6 Deposited 2023-09-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 6 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8U9Z Cdc48-Shp1 unfolding native substrate, Class 7 Deposited 2023-09-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 6 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UA0 Cdc48-Shp1 unfolding native substrate, Class 8 Deposited 2023-09-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 7 MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8UA1 Cdc48-Shp1 unfolding native substrate, Class 9 Deposited 2023-09-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 7 MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8UAA Cdc48-Shp1 unfolding native substrate, Class 3 Deposited 2023-09-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 8 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8UB4 Cdc48-Shp1 unfolding native substrate, consensus structure Deposited 2023-09-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 8 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric（64） Consistent with all polymers
Chain A 1–835（835 aa）
Chain B 1–835（835 aa）
Chain C 1–835（835 aa）
Chain D 1–835（835 aa）
Chain E 1–835（835 aa）
Chain F 1–835（835 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 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.