SAXSdb — 8dat

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

Cell division control protein 48

Saccharomyces cerevisiae

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain A； UniProt 1–835 Chain B； UniProt 1–835 Chain C； UniProt 1–835 Chain D； UniProt 1–835 Chain E； UniProt 1–835 Chain F； UniProt 1–835	Not recorded	Nuclear protein localization protein 4 × 1 （P33755） Ubiquitin fusion degradation protein 1 × 1 （P53044） Ubiquitin × 3 （P0CG63） 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

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 8DAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	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	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 1–835（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	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 1–835（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	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 1–835（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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–835（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	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	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	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	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
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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	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	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric	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

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDC48_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–838； UniProt 1–835 Author chain B； PDBConstruct 4–838； UniProt 1–835 Author chain C； PDBConstruct 4–838； UniProt 1–835 Author chain D； PDBConstruct 4–838； UniProt 1–835 Author chain E； PDBConstruct 4–838； UniProt 1–835 Author chain F； PDBConstruct 4–838； UniProt 1–835

Nuclear protein localization protein 4

Saccharomyces cerevisiae

UniProt P33755

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain G； UniProt 1–580	Not recorded	Cell division control protein 48 × 6 （P25694） Ubiquitin fusion degradation protein 1 × 1 （P53044） Ubiquitin × 3 （P0CG63） 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

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 8DAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6JWH Yeast Npl4 zinc finger, MPN and CTD domains Deposited 2019-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–580（468 aa）	Mutation：E123A,K124A,E125A	ZN ZINC ION × 2 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；4% Tacsimat (pH 6.0), 12% PEG 3350	Resolution 1.72 Å R-free 0.193
6JWI Yeast Npl4 in complex with Lys48-linked diubiquitin Deposited 2019-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 113–580（468 aa）	Not recorded	ZN ZINC ION × 2 BCN BICINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate	Resolution 2.55 Å R-free 0.226
6JWI Yeast Npl4 in complex with Lys48-linked diubiquitin Deposited 2019-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain E 113–580（468 aa）	Not recorded	ZN ZINC ION × 2 BCN BICINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate	Resolution 2.55 Å R-free 0.226
6JWJ Npl4 in complex with Ufd1 Deposited 2019-04-20	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 113–580（468 aa）	Mutation：E123A,K124A,E125A	ZN ZINC ION × 2 GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；90mM BisTris-HCl (pH 7.5), 19% PEG 3350, 10mM ATP	Resolution 1.58 Å R-free 0.206
6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 1–580（580 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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–580（580 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
8DAR Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP Deposited 2022-06-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–580（580 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	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 1–580（580 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
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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain G 1–580（580 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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain G 1–580（580 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	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 1–580（580 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
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric	Chain G 1–580（580 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

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NPL4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 4–583； UniProt 1–580

Ubiquitin fusion degradation protein 1

Saccharomyces cerevisiae

UniProt P53044

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain H； UniProt 1–361	Not recorded	Cell division control protein 48 × 6 （P25694） Nuclear protein localization protein 4 × 1 （P33755） Ubiquitin × 3 （P0CG63） 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

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 8DAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZC1 Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites Deposited 2005-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–208（208 aa） Fragment：N domain, residues 1-208	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；307 K；Ionic strength (raw mmCIF value) 20 mM Phosphate 50mM NaCl；Pressure 1 NMR sample composition 0.2mM Ufd1 \| 50mM Phosphate, 20mM NaCl,pH6.0	Resolution not provided
6JWJ Npl4 in complex with Ufd1 Deposited 2019-04-20	Different construct 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 C 288–305（18 aa）	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；90mM BisTris-HCl (pH 7.5), 19% PEG 3350, 10mM ATP	Resolution 1.58 Å R-free 0.206
8DAR Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP Deposited 2022-06-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–361（361 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	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain H 1–361（361 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
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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–361（361 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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–361（361 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	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–361（361 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

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UFD1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 3–363； UniProt 1–361

Ubiquitin

Saccharomyces cerevisiae

UniProt P0CG63

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain J； UniProt 1–76 Chain K； UniProt 1–76 Chain L； UniProt 1–76	Not recorded	Cell division control protein 48 × 6 （P25694） Nuclear protein localization protein 4 × 1 （P33755） Ubiquitin fusion degradation protein 1 × 1 （P53044） 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

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 8DAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3OLM Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT Ubiquitin Ligase Deposited 2010-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；13.5% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.272
4HCN Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin Deposited 2012-09-30	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 B 1–76（76 aa） Fragment：unp RESIDUES 1-76	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 FMT FORMIC ACID × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.2；293 K；12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K	Resolution 2.60 Å R-free 0.260
4NNJ Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin Deposited 2013-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–76（76 aa） Fragment：UNP residues 1-76 Chain D 1–76（76 aa） Fragment：UNP residues 1-76 Chain E 1–76（76 aa） Fragment：UNP residues 1-76	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 29 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15% (w/v) polyethylene glycol 3350, 100mM lithium sulfate and 100mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.201
4Q5E Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate Deposited 2014-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa）	Mutation：C17S, C137S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.87 Å R-free 0.232
4Q5H Shigella Effector Kinase OspG bound to AMPPNP and E2-Ub UbcH7-Ub Conjugate Deposited 2014-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa）	Mutation：C17S, C137S	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228
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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 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	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 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	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 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
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric	Chain H 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 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

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

View Construct and Data Evidence

UniProt name	UBI4P_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain K； PDBConstruct 1–76； UniProt 1–76 Author chain L； PDBConstruct 1–76； UniProt 1–76

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8dat
Deposition date deposition_date	2022-06-14
Structure title title	Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)
Keywords keywords	ATPASE, ATPASE COMPLEX, UBIQUITIN, SUMO, SMT3, QUALITY CONTROL, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	54.64 Å
Radius of gyration Rg (electron density) rg_electron	54.49 Å
Forward intensity I(0) i0	3565730000.00
Molecular weight molecular_weight	493660.0 kDa
Excluded volume excluded_volume	615150 Å³
Envelope volume envelope_volume	905650 Å³
Hydration-shell volume shell_volume	132600 Å³
Envelope diameter envelope_diameter	186.0 Å
Shell Rg shell_rg	62.12 Å
Envelope Rg envelope_rg	53.91 Å
Shape Rg shape_rg	54.53 Å
Total Rg total_rg	54.54 Å
Total atoms total_atoms	34635
Residues n_residues	4388
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	178.9 Å
Rg (real space) rg_real	54.47 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	3.5660e+09
I(0) uncertainty (real space) i0_real_error	6.5380e+07
Rg (reciprocal space) rg_reciprocal	54.78 Å
I(0) (reciprocal space) i0_reciprocal	3567000000.0000
Solution quality estimate total_estimate	0.8617
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.8 Å
Skewness Skewness skewness	0.265
Kurtosis Kurtosis kurtosis	-0.251
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	623500000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.730

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Cell division control protein 48
Molecular weight formula_weight	92389.2 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	34635

GSHMGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear protein localization protein 4
Molecular weight formula_weight	66144.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GSHMLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELADRTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin fusion degradation protein 1
Molecular weight formula_weight	40001.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GSMFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYKALKAQQDKEKKNSFGKGQVLDPSVLGQGSMSTRIDYAGIANSSRNKLSKFVGQGQNISGKAPKAEPKQDIKDMKITFDGEPAKLDLPEGQLFFGFPMVLPKEDEESAAGSKSSEQNFQGQGISLRKSNKRKTKSDHDSSKSKAPKSPEVIEID

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8568.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L

MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

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

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	8datJ01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	8datK01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	8datL01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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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	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	22510

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

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)

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

Cell division control protein 48

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear protein localization protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin fusion degradation protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)