9mpr

Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP

Method: ELECTRON MICROSCOPY D_max: 148.3 Å Quality: GOOD

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

Deubiquitinating protein VCPIP1

Homo sapiens

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain G； UniProt 1–1222 Chain H； UniProt 1–1222 Chain I； UniProt 1–1222	Not recorded	Transitional endoplasmic reticulum ATPase × 6 （P55072）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.90 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 9MPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YKA Cryo-EM structure of P97-VCPIP1 complex Deposited 2024-03-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain 1 105–673（569 aa） Chain 2 105–673（569 aa） Chain 3 105–673（569 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9DIL Cryo-EM structure of VCP/p97 in complex with VCPIP1 (VCIP135) Deposited 2024-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–1222（1222 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9MPS Cryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (with extra D2 domain) Deposited 2024-12-31	Different construct Different mutation/modification Different oligomeric state	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–1222（1222 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9MPT Cryo-EM structure of VCPIP1 UBX domain bound to VCP N-domain (with D1 domain) Deposited 2024-12-31	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–1222（1222 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9MPV Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP Deposited 2024-12-31	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 1–1222（1222 aa） Chain H 1–1222（1222 aa） Chain I 1–1222（1222 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9MQ6 Cryo-EM structure of VCP/p97 and VCPIP1 (VCIP135) in the presence of AMPPNP Deposited 2025-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–1222（1222 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VCIP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 29–1250； UniProt 1–1222 Author chain H； PDBConstruct 29–1250； UniProt 1–1222 Author chain I； PDBConstruct 29–1250； UniProt 1–1222

Transitional endoplasmic reticulum ATPase

Homo sapiens

UniProt P55072

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 1–806 Chain B； UniProt 1–806 Chain C； UniProt 1–806 Chain D； UniProt 1–806 Chain E； UniProt 1–806 Chain F； UniProt 1–806	Not recorded	Deubiquitinating protein VCPIP1 × 3 （Q96JH7）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10QQ Structure of human VCP/p97 dodecamer bound to ADP (DMSO control) Deposited 2026-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 24 MG MAGNESIUM ION × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES-KOH pH 7.4, 100 mM KOAc, 10mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.13 Å
10QR Structure of human VCP/p97 hexamer bound to ADP (DMSO control) Deposited 2026-02-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES-KOH pH 7.4, 100mM KOAc, 10mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
11TA Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused) Deposited 2026-03-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；50 mM HEPES, pH 7.6, 150 mM KCl, 5 mM MgCl2, 2 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
11VE Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1) Deposited 2026-03-13	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å
3EBB PLAP/P97 complex Deposited 2008-08-27	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 × 4 PDB declaration: tetrameric	Chain E 797–806（10 aa） Fragment：C-TERMINAL PEPTIDE, residues 797-806 Chain F 797–806（10 aa） Fragment：C-TERMINAL PEPTIDE, residues 797-806	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.1 M TRIS, PH 8.50, 0.2 M MGCL2, , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.248
3EBB PLAP/P97 complex Deposited 2008-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 797–806（10 aa） Fragment：C-TERMINAL PEPTIDE, residues 797-806 Chain H 797–806（10 aa） Fragment：C-TERMINAL PEPTIDE, residues 797-806	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.1 M TRIS, PH 8.50, 0.2 M MGCL2, , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.248
3HU1 Structure of p97 N-D1 R95G mutant in complex with ATPgS Deposited 2009-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：residues 1-481 Chain B 1–481（481 aa） Fragment：residues 1-481 Chain C 1–481（481 aa） Fragment：residues 1-481 Chain D 1–481（481 aa） Fragment：residues 1-481 Chain E 1–481（481 aa） Fragment：residues 1-481 Chain F 1–481（481 aa） Fragment：residues 1-481	Mutation：R95G Mutation：R95G Mutation：R95G Mutation：R95G Mutation：R95G Mutation：R95G	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；288 K；100mM NaCl, 4% benzamidine, 100mM citrate, pH 5.8, 16.5% PEG3350 and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.81 Å R-free 0.271
3HU2 Structure of p97 N-D1 R86A mutant in complex with ATPgS Deposited 2009-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：residues 1-481 Chain B 1–481（481 aa） Fragment：residues 1-481 Chain C 1–481（481 aa） Fragment：residues 1-481 Chain D 1–481（481 aa） Fragment：residues 1-481 Chain E 1–481（481 aa） Fragment：residues 1-481 Chain F 1–481（481 aa） Fragment：residues 1-481	Mutation：R86G Mutation：R86G Mutation：R86G Mutation：R86G Mutation：R86G Mutation：R86G	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；288 K；100mM NaCl, 4% benzamidine, 100mM citrate, pH 5.8, 16.5% PEG3350 and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.85 Å R-free 0.290
3HU3 Structure of p97 N-D1 R155H mutant in complex with ATPgS Deposited 2009-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：residues 1-481 Chain B 1–481（481 aa） Fragment：residues 1-481	Mutation：R155H Mutation：R155H	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；288 K；100mM citrate buffer pH 5.6, 6% benzamidine, 7% PEG3350, and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.20 Å R-free 0.193
3QC8 Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change Deposited 2011-01-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–196（176 aa） Fragment：N domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；25%(w/v) PEG3350, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.250
3QQ7 Crystal Structure of the p97 N-terminal domain Deposited 2011-02-15	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 2–187（186 aa） Fragment：unp residues 2-187	Not recorded	HEZ HEXANE-1,6-DIOL × 1 GOL GLYCEROL × 1 CO COBALT (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；1 M Hexanediol, 0.1 M Na-acetate, 0.01 M CoCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.235
3QQ8 Crystal structure of p97-N in complex with FAF1-UBX Deposited 2011-02-15	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 2–187（186 aa） Fragment：unp residues 2-187	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16-20% PEG MME 2000, 0.2 M Trimethyl-N-oxide, 0.1 M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.5	Resolution 2.00 Å R-free 0.210
3QWZ Crystal structure of FAF1 UBX-p97N-domain complex Deposited 2011-02-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–208（208 aa） Fragment：UNP residues 1-208	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；295 K；30% PEG 3000, 0.1M sodium acetate, 1M lithium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 2.00 Å R-free 0.249
3QWZ Crystal structure of FAF1 UBX-p97N-domain complex Deposited 2011-02-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–208（208 aa） Fragment：UNP residues 1-208	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；295 K；30% PEG 3000, 0.1M sodium acetate, 1M lithium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 2.00 Å R-free 0.249
3TIW Crystal structure of p97N in complex with the C-terminus of gp78 Deposited 2011-08-22	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 1–187（187 aa） Fragment：unp residues 1-187	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；18-22% (w/v) polyethylene glycol 3000, 0.2 M NaCl and 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.171
3TIW Crystal structure of p97N in complex with the C-terminus of gp78 Deposited 2011-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–187（187 aa） Fragment：unp residues 1-187	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；18-22% (w/v) polyethylene glycol 3000, 0.2 M NaCl and 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.171
4KDI Crystal structure of p97/VCP N in complex with OTU1 UBXL Deposited 2013-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–196（176 aa） Fragment：N domain (Residues 21-185)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；20% PEG 2000, 10% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.86 Å R-free 0.257
4KDI Crystal structure of p97/VCP N in complex with OTU1 UBXL Deposited 2013-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–196（176 aa） Fragment：N domain (Residues 21-185)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；20% PEG 2000, 10% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.86 Å R-free 0.257
4KDL Crystal structure of p97/VCP N in complex with OTU1 UBXL Deposited 2013-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–196（176 aa） Fragment：N domain (Residues 23-196)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；14% PEG 4000, 0.1 M Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.81 Å R-free 0.213
4KDL Crystal structure of p97/VCP N in complex with OTU1 UBXL Deposited 2013-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–196（176 aa） Fragment：N domain (Residues 23-196)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；14% PEG 4000, 0.1 M Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.81 Å R-free 0.213
4KLN Structure of p97 N-D1 A232E mutant in complex with ATPgS Deposited 2013-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：UNP residue 1-481 Chain B 1–481（481 aa） Fragment：UNP residue 1-481 Chain C 1–481（481 aa） Fragment：UNP residue 1-481 Chain D 1–481（481 aa） Fragment：UNP residue 1-481 Chain E 1–481（481 aa） Fragment：UNP residue 1-481 Chain F 1–481（481 aa） Fragment：UNP residue 1-481	Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；288 K；0.1M citrate, pH 5.8, 0.3M NaCl, 13.6% PEG 3350, 20% glycerol, 0.525% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.62 Å R-free 0.289
4KO8 Structure of p97 N-D1 R155H mutant in complex with ATPgS Deposited 2013-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：UNP residue 1-481 Chain B 1–481（481 aa） Fragment：UNP residue 1-481	Mutation：R155H Mutation：R155H	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；288 K；100mM citrate buffer pH 5.6, 6% benzamidine, 7% PEG3350, and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.98 Å R-free 0.205
4KOD Structure of p97 N-D1 R155H mutant in complex with ADP Deposited 2013-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：UNP residue 1-481 Chain B 1–481（481 aa） Fragment：UNP residue 1-481 Chain C 1–481（481 aa） Fragment：UNP residue 1-481 Chain D 1–481（481 aa） Fragment：UNP residue 1-481 Chain E 1–481（481 aa） Fragment：UNP residue 1-481 Chain F 1–481（481 aa） Fragment：UNP residue 1-481	Mutation：R155HH Mutation：R155HH Mutation：R155HH Mutation：R155HH Mutation：R155HH Mutation：R155HH	ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；288 K；0.1M citrate, pH 5.8, 0.3M NaCl, 13.6% EPG 3350, 20% glycerol, 0.625% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.96 Å R-free 0.291
4KOD Structure of p97 N-D1 R155H mutant in complex with ADP Deposited 2013-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 1–481（481 aa） Fragment：UNP residue 1-481 Chain H 1–481（481 aa） Fragment：UNP residue 1-481 Chain I 1–481（481 aa） Fragment：UNP residue 1-481 Chain J 1–481（481 aa） Fragment：UNP residue 1-481 Chain K 1–481（481 aa） Fragment：UNP residue 1-481 Chain L 1–481（481 aa） Fragment：UNP residue 1-481	Mutation：R155HH Mutation：R155HH Mutation：R155HH Mutation：R155HH Mutation：R155HH Mutation：R155HH	ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；288 K；0.1M citrate, pH 5.8, 0.3M NaCl, 13.6% EPG 3350, 20% glycerol, 0.625% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.96 Å R-free 0.291
4P0A Crystal structure of HOIP PUB domain in complex with p97 PIM Deposited 2014-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 797–806（10 aa） Fragment：UNP Residues 797-806	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 6.5	Resolution 2.30 Å R-free 0.249
4P0A Crystal structure of HOIP PUB domain in complex with p97 PIM Deposited 2014-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 797–806（10 aa） Fragment：UNP Residues 797-806	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 6.5	Resolution 2.30 Å R-free 0.249
5B6C Structural Details of Ufd1 binding to p97 Deposited 2016-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–191（171 aa） Fragment：UNP residues 21-191	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；21%(w/v) PEG 8000, 2.9mM n-nonyl-beta-thiomaltoside, 0.1M HEPES, pH 7.5	Resolution 1.55 Å R-free 0.200
5C18 p97-delta709-728 in complex with ATP-gamma-S Deposited 2015-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；6.5-7% PEG 4000, 0.4-0.6 M potassium acetate, 0.1 M MES pH 5.75	Resolution 3.30 Å R-free 0.249
5C19 p97 variant 2 in the apo state Deposited 2015-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；12% PEG 4000, 0.15 M ammonium sulfate, 0.1 M MES pH 6.5	Resolution 4.20 Å R-free 0.302
5C1A p97-N750D/R753D/M757D/Q760D in complex with ATP-gamma-S Deposited 2015-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；9-9.5% PEG 4000, 0.4-0.5 M magnesium acetate, 0.1 M sodium-citrate pH 5.6	Resolution 3.80 Å R-free 0.254
5C1A p97-N750D/R753D/M757D/Q760D in complex with ATP-gamma-S Deposited 2015-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 2–806（805 aa） Chain H 2–806（805 aa） Chain I 2–806（805 aa） Chain J 2–806（805 aa） Chain K 2–806（805 aa） Chain L 2–806（805 aa）	Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D Mutation：N750D, R753D, M757D, Q760D	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；9-9.5% PEG 4000, 0.4-0.5 M magnesium acetate, 0.1 M sodium-citrate pH 5.6	Resolution 3.80 Å R-free 0.254
5C1B p97-delta709-728 in complex with a UFD1-SHP peptide Deposited 2015-06-13	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 × 8 PDB declaration: octameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion Mutation：709-728 deletion	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12 CL CHLORIDE ION × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；6.5-7% PEG 4000, 0.4-0.6 M potassium acetate, 0.1 M MES pH 5.75	Resolution 3.08 Å R-free 0.240
5DYG Structure of p97 N-D1 L198W mutant in complex with ADP Deposited 2015-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–460（460 aa） Fragment：UNP residues 1-460	Mutation：L198W	ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；3.7 M sodium formate, pH 6.0, 8 % glycerol	Resolution 2.20 Å R-free 0.258
5DYI Structure of p97 N-D1 wild-type in complex with ADP Deposited 2015-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–481（481 aa） Fragment：UNP residues 1-481 Chain B 1–481（481 aa） Fragment：UNP residues 1-481 Chain C 1–481（481 aa） Fragment：UNP residues 1-481 Chain D 1–481（481 aa） Fragment：UNP residues 1-481 Chain E 1–481（481 aa） Fragment：UNP residues 1-481 Chain F 1–481（481 aa） Fragment：UNP residues 1-481	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.1 M sodium citrate, pH 6.0, 0.3 M NaCl, 15.2 % PEG3350, 20 % glycerol, 2 % benzamidine	Resolution 3.71 Å R-free 0.285
5DYI Structure of p97 N-D1 wild-type in complex with ADP Deposited 2015-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 1–481（481 aa） Fragment：UNP residues 1-481 Chain H 1–481（481 aa） Fragment：UNP residues 1-481 Chain I 1–481（481 aa） Fragment：UNP residues 1-481 Chain J 1–481（481 aa） Fragment：UNP residues 1-481 Chain K 1–481（481 aa） Fragment：UNP residues 1-481 Chain L 1–481（481 aa） Fragment：UNP residues 1-481	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.1 M sodium citrate, pH 6.0, 0.3 M NaCl, 15.2 % PEG3350, 20 % glycerol, 2 % benzamidine	Resolution 3.71 Å R-free 0.285
5EPP Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in Rhomboid Protease, RHBDL4 Deposited 2015-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–199（179 aa） Fragment：UNP RESIDUES 21-199	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG 3350, 0.1 M Bis-Tris Propane pH 6.5, 0.2 M Sodium Acetate	Resolution 1.88 Å R-free 0.209
5FTJ Cryo-EM structure of human p97 bound to UPCDC30245 inhibitor Deposited 2016-01-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 OJA 1-(3-(5-FLUORO-1H-INDOL-2-YL)PHENYL)PIPERIDIN-4-YL)(2-(4-ISOPROPYL-PIPERAZIN1-YL)ETHYL)-CARBAMATE × 6	ELECTRON MICROSCOPY cryo-EM buffer 25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP；pH 8；25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90.15, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING.	Resolution 2.30 Å
5FTK Cryo-EM structure of human p97 bound to ADP Deposited 2016-01-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer 25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP；pH 8；25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90.15, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING.	Resolution 2.40 Å
5FTL Cryo-EM structure of human p97 bound to ATPgS (Conformation I) Deposited 2016-01-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer 25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP；pH 8；25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90.15, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING.	Resolution 3.30 Å
5FTM Cryo-EM structure of human p97 bound to ATPgS (Conformation II) Deposited 2016-01-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer 25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP；pH 8；25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90.15, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING.	Resolution 3.20 Å
5FTN Cryo-EM structure of human p97 bound to ATPgS (Conformation III) Deposited 2016-01-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer 25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP；pH 8；25 MM TRIS, 150 MM NACL, 1 MM MGCL2, 1.0 MM TCEP cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90.15, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING.	Resolution 3.30 Å
5GLF Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–199（179 aa） Fragment：P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG 3350, BIS-TRIS PH 6.5, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 2.25 Å R-free 0.230
5GLF Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 21–199（179 aa） Fragment：P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG 3350, BIS-TRIS PH 6.5, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 2.25 Å R-free 0.230
5GLF Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 21–199（179 aa） Fragment：P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG 3350, BIS-TRIS PH 6.5, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 2.25 Å R-free 0.230
5GLF Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 21–199（179 aa） Fragment：P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG 3350, BIS-TRIS PH 6.5, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 2.25 Å R-free 0.230
5IFS Quantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death Deposited 2016-02-26	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 × 4 PDB declaration: tetrameric	Chain B 1–481（481 aa） Chain D 1–481（481 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；23% PEG3350, 0.3M LiSO4, 0.1M Hepes pH 7.0	Resolution 2.46 Å R-free 0.251
5IFW Quantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death Deposited 2016-02-26	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 × 4 PDB declaration: tetrameric	Chain B 2–806（805 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5	Resolution 3.40 Å R-free 0.261
5KIW p97 ND1-L198W in complex with VIMP Deposited 2016-06-17	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 × 4 PDB declaration: tetrameric	Chain A 1–460（460 aa） Fragment：N-terminal residues 1-460 Chain B 1–460（460 aa） Fragment：N-terminal residues 1-460	Mutation：L198W Mutation：L198W	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；288 K；0.1 M Tris, pH 8, 15 % ethanol, 100 mM NaCl, 7 % MPD	Resolution 3.41 Å R-free 0.294
5KIY p97 ND1-A232E in complex with VIMP Deposited 2016-06-17	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 × 12 PDB declaration: dodecameric	Chain A 1–460（460 aa） Fragment：N-terminal residues 1-460	Mutation：A232E	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；0.1 M Tris, pH 8, 6-7 % ethanol, 100 mM NaCl, 3.6-4.2 % MPD	Resolution 2.79 Å R-free 0.256
5X4L Crystal structure of the UBX domain of human UBXD7 in complex with p97 N domain Deposited 2017-02-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–196（174 aa） Fragment：UNP residues 23-196	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；0.2M Calcium acetate hydrate pH7.5, 20% v/v PEG 3350	Resolution 2.40 Å R-free 0.234
5X4L Crystal structure of the UBX domain of human UBXD7 in complex with p97 N domain Deposited 2017-02-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–196（174 aa） Fragment：UNP residues 23-196	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；0.2M Calcium acetate hydrate pH7.5, 20% v/v PEG 3350	Resolution 2.40 Å R-free 0.234
6G2V Crystal structure of the p97 D2 domain in a helical split-washer conformation Deposited 2018-03-23	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 462–764（303 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5	Resolution 1.90 Å R-free 0.237
6G2W Crystal structure of the p97 D2 domain in a helical split-washer conformation Deposited 2018-03-23	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 462–764（303 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 1 AWD ~{N}-(4-fluorophenyl)-4-methyl-piperazine-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5	Resolution 2.68 Å R-free 0.324
6G2X Crystal structure of the p97 D2 domain in a helical split-washer conformation Deposited 2018-03-23	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 462–764（303 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 EJQ ~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5	Resolution 2.08 Å R-free 0.245
6G2Y Crystal structure of the p97 D2 domain in a helical split-washer conformation Deposited 2018-03-23	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 462–764（303 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 1 ELQ [3,4-bis(fluoranyl)phenyl]-(4-methylpiperazin-1-yl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5	Resolution 2.15 Å R-free 0.247
6G2Z Crystal structure of the p97 D2 domain in a helical split-washer conformation Deposited 2018-03-23	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 462–764（303 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 1 EJW (3-phenyl-1,2-oxazol-5-yl)methylazanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5	Resolution 1.92 Å R-free 0.247
6G30 Crystal structure of the p97 D2 domain in a helical split-washer conformation Deposited 2018-03-23	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 462–764（303 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 1 ELN ~{N}-(4-chlorophenyl)-2-cyano-ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5	Resolution 2.42 Å R-free 0.273
6HD0 Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1 Deposited 2018-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–481（481 aa） Chain B 1–481（481 aa） Chain C 1–481（481 aa） Chain T 1–481（481 aa） Chain U 1–481（481 aa） Chain V 1–481（481 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；6% (v/v) PEG1500, 0.2M sodium acetate, 0.1M Hepes pH 7.0	Resolution 3.73 Å R-free 0.253
6MCK p97 D1D2 with CB5083 bound Deposited 2018-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 210–806（597 aa） Chain B 210–806（597 aa） Chain C 210–806（597 aa） Chain D 210–806（597 aa） Chain E 210–806（597 aa） Chain F 210–806（597 aa） Chain G 210–806（597 aa） Chain H 210–806（597 aa） Chain I 210–806（597 aa） Chain J 210–806（597 aa） Chain K 210–806（597 aa） Chain L 210–806（597 aa）	Not recorded	JDP 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；289 K；0.1 M sodium citrate, pH 4.5, 250 mM Tri-sodium citrate and 15 % PEG3350	Resolution 3.77 Å R-free 0.265
7BP8 Human AAA+ ATPase VCP mutant - T76A, ADP-bound form Deposited 2020-03-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：T76A Mutation：T76A Mutation：T76A Mutation：T76A Mutation：T76A Mutation：T76A	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7BP9 Human AAA+ ATPase VCP mutant - T76E, ADP-bound form Deposited 2020-03-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：T76E Mutation：T76E Mutation：T76E Mutation：T76E Mutation：T76E Mutation：T76E	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7BPA Human AAA+ ATPase VCP mutant - T76A, AMP-PNP-bound form, Conformation I Deposited 2020-03-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：T76A Mutation：T76A Mutation：T76A Mutation：T76A Mutation：T76A Mutation：T76A	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7BPB Human AAA+ ATPase VCP mutant - T76E, AMP-PNP bound form, Conformation I Deposited 2020-03-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：T76E Mutation：T76E Mutation：T76E Mutation：T76E Mutation：T76E Mutation：T76E	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7JY5 Structure of human p97 in complex with ATPgammaS and Npl4/Ufd1 (masked around p97) Deposited 2020-08-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	MG MAGNESIUM ION × 12 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
7K56 Structure of VCP dodecamer purified from H1299 cells Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20mM Hepes pH7.4, 150mM NaCl, 1mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；3.5ul sample was applied to a lacy carbon grid coated with graphene oxide. 7 seconds blot with filter paper was performed using Gatan Cp3.	Resolution 3.90 Å
7K57 Structure of apo VCP dodecamer generated from bacterially recombinant VCP/p97 Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20mM Hepes pH7.4, 150mM NaCl, 1mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；3.5ul sample was applied to a lacy carbon grid coated with graphene oxide. 7 seconds blot with filter paper was performed using Gatan Cp3.	Resolution 3.70 Å
7K59 Structure of apo VCP hexamer generated from bacterially recombinant VCP/p97 Deposited 2020-09-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20mM Hepes pH7.4, 150mM NaCl, 1mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；3.5ul sample was applied to a lacy carbon grid coated with graphene oxide. 7 seconds blot with filter paper was performed using Gatan Cp3.	Resolution 4.20 Å
7L5W p97-R155H mutant dodecamer I Deposited 2020-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；The grid was blotted for 6 seconds.	Resolution 3.34 Å
7L5X p97-R155H mutant dodecamer II Deposited 2020-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；The grid was blotted for 6 seconds.	Resolution 6.10 Å
7LMY Cryo-EM structure of human p97 in complex with NMS-873 in the presence of ATP, Npl4/Ufd1, and Ub6 Deposited 2021-02-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ATP ADENOSINE-5'-TRIPHOSPHATE × 12 Y6Y 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine × 6 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
7LMZ Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 1) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.06 Å
7LN0 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 2) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
7LN1 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 3) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7LN2 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 1) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.63 Å
7LN3 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 2) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
7LN4 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 3) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7LN5 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (CHAPSO, Class 1, Close State) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
7LN6 Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (CHAPSO, Class 2, Open State) Deposited 2021-02-06	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 A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q Mutation：A232E/E578Q	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
7MDM Structure of human p97 ATPase L464P mutant Deposited 2021-04-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.86 Å
7MDO Structure of human p97 ATPase L464P mutant Deposited 2021-04-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
7MHS Structure of p97 (subunits A to E) with substrate engaged Deposited 2021-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 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 3.60 Å
7OAT Structural basis for targeted p97 remodelling by ASPL as prerequisite for p97 trimethylation by METTL21D Deposited 2021-04-20	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 × 3 PDB declaration: trimeric	Chain B 2–480（479 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；16% PEG 8000, 0.2 M calcium acetate, 0.1 M MES (pH 6.5)	Resolution 3.00 Å R-free 0.270
7PUX Structure of p97 N-D1(L198W) in complex with Fragment TROLL2 Deposited 2021-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–460（460 aa）	Mutation：L198W	ADP ADENOSINE-5'-DIPHOSPHATE × 6 FMT FORMIC ACID × 96 6LY (1S)-2-amino-1-(4-bromophenyl)ethan-1-ol × 6 PEG DI(HYDROXYETHYL)ETHER × 6 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；Natriumformiat (pH 6.0) 4.0 M Glycerol (v/v) 10 % PEG 600 (v/v) 5 %	Resolution 1.73 Å R-free 0.235
7R7S p47-bound p97-R155H mutant with ATPgammaS Deposited 2021-06-25	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；The grid was blotted for 6 seconds.	Resolution 4.23 Å
7R7T p47-bound p97-R155H mutant with ADP Deposited 2021-06-25	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；The grid was blotted for 6 seconds.	Resolution 4.50 Å
7R7U D1 and D2 domain structure of the p97(R155H)-p47 complex Deposited 2021-06-25	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7RL6 Cryo-EM structure of human p97-R155H mutant bound to ADP. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ADP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7RL7 Cryo-EM structure of human p97-R155H mutant bound to ATPgS. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ATPgS. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7RL9 Cryo-EM structure of human p97-R191Q mutant bound to ADP. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：R191Q Mutation：R191Q Mutation：R191Q Mutation：R191Q Mutation：R191Q Mutation：R191Q	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ADP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7RLA Cryo-EM structure of human p97-R191Q mutant bound to ATPgS. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：R191Q Mutation：R191Q Mutation：R191Q Mutation：R191Q Mutation：R191Q Mutation：R191Q	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ATPgS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7RLB Cryo-EM structure of human p97-A232E mutant bound to ADP Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ADP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7RLC Cryo-EM structure of human p97-A232E mutant bound to ATPgS. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E Mutation：A232E	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ADP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7RLD Cryo-EM structure of human p97-E470D mutant bound to ADP. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：E470D Mutation：E470D Mutation：E470D Mutation：E470D Mutation：E470D Mutation：E470D	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ADP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7RLF Cryo-EM structure of human p97-E470D mutant bound to ATPgS. Deposited 2021-07-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：E470D Mutation：E470D Mutation：E470D Mutation：E470D Mutation：E470D Mutation：E470D	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ATPgS. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7RLG Cryo-EM structure of human p97-D592N mutant bound to ADP. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Mutation：D592N Mutation：D592N Mutation：D592N Mutation：D592N Mutation：D592N Mutation：D592N	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ADP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7RLH Cryo-EM structure of human p97-D592N mutant bound to ATPgS. Deposited 2021-07-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：D592N Mutation：D592N Mutation：D592N Mutation：D592N Mutation：D592N Mutation：D592N	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ATPgS. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7RLI Cryo-EM structure of human p97 bound to CB-5083 and ADP. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa） Chain G 2–806（805 aa） Chain H 2–806（805 aa） Chain I 2–806（805 aa） Chain J 2–806（805 aa） Chain K 2–806（805 aa） Chain L 2–806（805 aa）	Not recorded	JDP 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer and CB-5083 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7RLJ Cryo-EM structure of human p97 bound to CB-5083 and ATPgS. Deposited 2021-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 21–775（755 aa） Chain B 21–775（755 aa） Chain C 21–775（755 aa） Chain D 21–775（755 aa） Chain E 21–775（755 aa） Chain F 21–775（755 aa） Chain G 21–775（755 aa） Chain H 21–775（755 aa） Chain I 21–775（755 aa） Chain J 21–775（755 aa） Chain K 21–775（755 aa） Chain L 21–775（755 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12 JDP 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Protein Storage Buffer with ATPgS and CB-5083. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7VCS Human p97 double hexamer conformer II with ATPgammaS bound Deposited 2021-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 24 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 5 mM MgCl2, 0.5 mM TCEP, 0.01% NP40 cryo-EM vitrification conditions Cryogen ETHANE；3ul sample was applied and the grids were blotted for 3.0 s under 100% humidity at 277K before being plunged into liquid ethane using a Mark IV Vitrobot (FEI).	Resolution 3.32 Å
7VCT Human p97 single hexamer conformer III with D1-ATPgammaS and D2-ADP bound Deposited 2021-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 5 mM MgCl2, 0.5 mM TCEP, 0.01% NP40 cryo-EM vitrification conditions Cryogen ETHANE；3ul sample was applied and the grids were blotted for 3.0 s under 100% humidity at 277K before being plunged into liquid ethane using a Mark IV Vitrobot (FEI).	Resolution 3.21 Å
7VCU Human p97 double hexamer conformer I with D1-ATPgammaS and D2-ADP bound Deposited 2021-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 5 mM MgCl2, 0.5 mM TCEP, 0.01% NP40 cryo-EM vitrification conditions Cryogen ETHANE；3ul sample was applied and the grids were blotted for 3.0 s under 100% humidity at 277K before being plunged into liquid ethane using a Mark IV Vitrobot (FEI).	Resolution 3.15 Å
7VCV Human p97 single hexamer conformer I with ATPgammaS bound Deposited 2021-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 5 mM MgCl2, 0.5 mM TCEP, 0.01% NP40 cryo-EM vitrification conditions Cryogen ETHANE；3ul sample was applied and the grids were blotted for 3.0 s under 100% humidity at 277K before being plunged into liquid ethane using a Mark IV Vitrobot (FEI).	Resolution 3.21 Å
7VCX Human p97 single hexamer conformer II with ATPgammaS bound Deposited 2021-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 5 mM MgCl2, 0.5 mM TCEP, 0.01% NP40 cryo-EM vitrification conditions Cryogen ETHANE；3ul sample was applied and the grids were blotted for 3.0 s under 100% humidity at 277K before being plunged into liquid ethane using a Mark IV Vitrobot (FEI).	Resolution 3.24 Å
7WUB Cryo-EM structure of dodecamer P97 Deposited 2022-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 21–775（755 aa） Chain B 21–775（755 aa） Chain C 200–775（576 aa） Chain D 200–775（576 aa） Chain E 21–775（755 aa） Chain F 21–775（755 aa） Chain G 21–775（755 aa） Chain H 21–775（755 aa） Chain I 21–775（755 aa） Chain J 21–775（755 aa） Chain K 21–775（755 aa） Chain L 21–775（755 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 Y6Y 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7Y4W The cryo-EM structure of human ERAD retro-translocation complex Deposited 2022-06-16	Different construct 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 21–806（786 aa） Chain B 21–806（786 aa） Chain C 21–806（786 aa） Chain D 21–806（786 aa） Chain E 21–806（786 aa） Chain F 21–806（786 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
7Y53 The cryo-EM structure of human ERAD retro-translocation complex Deposited 2022-06-16	Different construct 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 21–806（786 aa） Chain B 21–806（786 aa） Chain C 21–806（786 aa） Chain D 21–806（786 aa） Chain E 21–806（786 aa） Chain F 21–806（786 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.61 Å
7Y59 The cryo-EM structure of human ERAD retro-translocation complex Deposited 2022-06-16	Different construct 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 21–806（786 aa） Chain B 21–806（786 aa） Chain C 21–806（786 aa） Chain D 21–806（786 aa） Chain E 21–806（786 aa） Chain F 21–806（786 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.51 Å
8B5R p97-p37-SPI substrate complex Deposited 2022-09-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
8FCL Cryo-EM structure of p97:UBXD1 closed state Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 3.51 Å
8FCM Cryo-EM structure of p97:UBXD1 open state Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 3.27 Å
8FCN Cryo-EM structure of p97:UBXD1 VIM-only state Deposited 2022-12-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 2.95 Å
8FCO Cryo-EM structure of p97:UBXD1 meta state Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 3.31 Å
8FCP Cryo-EM structure of p97:UBXD1 para state Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 3.52 Å
8FCQ Cryo-EM structure of p97:UBXD1 PUB-in state Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 3.93 Å
8FCR Cryo-EM structure of p97:UBXD1 H4-bound state Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 3 sec, blot force 0	Resolution 4.12 Å
8FCT Cryo-EM structure of p97:UBXD1 lariat mutant Deposited 2022-12-01	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 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 sec, blot time 4 sec, blot force 0	Resolution 3.42 Å
8HL7 Crystal structure of p97 N/D1 in complex with a valosin-containing protein methyltransferase Deposited 2022-11-29	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 23–458（436 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 3 FMT FORMIC ACID × 2 ACT ACETATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；20 % (w/v) polyethylene glycol (PEG) 3350, 0.1M Na-HEPES (pH 7.5), 2 % (v/v) Tacsimate (pH 7.0), and 3 % (w/v) 6-aminohexanoic acid	Resolution 2.80 Å R-free 0.261
8HRZ Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains Deposited 2022-12-16	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 × 24 PDB declaration: 24-meric	Chain A 21–458（438 aa） Chain B 21–458（438 aa） Chain C 21–458（438 aa） Chain D 21–458（438 aa） Chain E 21–458（438 aa） Chain F 21–458（438 aa） Chain G 21–458（438 aa） Chain H 21–458（438 aa） Chain I 21–458（438 aa） Chain J 21–458（438 aa） Chain K 21–458（438 aa） Chain L 21–458（438 aa）	Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A Mutation：E294A, K295A	ADP ADENOSINE-5'-DIPHOSPHATE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；14% PEG 3350, 0.2M ammonium citrate tribasic (pH 7), 0.01M hexamine cobalt (III) chloride	Resolution 2.70 Å R-free 0.256
8KG2 Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain Deposited 2023-08-17	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 × 24 PDB declaration: 24-meric	Chain A 21–458（438 aa） Chain B 21–458（438 aa） Chain C 21–458（438 aa） Chain D 21–458（438 aa） Chain E 21–458（438 aa） Chain F 21–458（438 aa） Chain G 21–458（438 aa） Chain H 21–458（438 aa） Chain I 21–458（438 aa） Chain J 21–458（438 aa） Chain K 21–458（438 aa） Chain L 21–458（438 aa）	Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A Mutation：E192A, D193A, E194A	ADP ADENOSINE-5'-DIPHOSPHATE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；0.2M sodium acetate, 0.1M sodium citrate (pH 5.6), 5% polyethylene glycol 4000	Resolution 3.10 Å R-free 0.246
8OOI Full composite cryo-EM map of p97/VCP in ADP.Pi state Deposited 2023-04-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 12 K POTASSIUM ION × 6 PO4 PHOSPHATE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
8PQX p97 (VCP) mutant - F539A state III Deposited 2023-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；pre-blotting incubation time of 20 seconds and blot for 2.0 seconds with -1 blot force	Resolution 3.30 Å
8R0E p97 (VCP) mutant - F266A Deposited 2023-10-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；pre-blotting incubation time of 20 secounds and blot for 3.5 seconds with -1 blot force	Resolution 2.70 Å
8RS9 p97 (VCP) double mutant - F266A F539A Deposited 2024-01-24	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；pre-blotting incubation time of 20 secounds and blot for 3.5 seconds with -1 blot force	Resolution 3.40 Å
8RSB p97 (VCP) mutant - F539A ADP state Deposited 2024-01-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；pre-blotting incubation time of 20 secounds and blot for 3.5 seconds with -1 blot force	Resolution 3.40 Å
8RSC p97 (VCP) mutant - F539A Deposited 2024-01-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；pre-blotting incubation time of 20 secounds and blot for 3.5 seconds with -1 blot force	Resolution 3.60 Å
8UV2 Human p97/VCP structure with a triazole inhibitor (NSC799462/hexamer) Deposited 2023-11-02	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 XKM 3-(2,6-difluoro-4-{[(4P)-5-{[(2S)-hexan-2-yl]sulfanyl}-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}phenyl)prop-2-yn-1-yl (1-methylpiperidin-4-yl)carbamate × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8UVO Human p97/VCP R155H mutant structure with a triazole inhibitor (NSC804515) Deposited 2023-11-03	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	ADP ADENOSINE-5'-DIPHOSPHATE × 12 XNU N-[3-(2,5-difluoro-4-{[(4M)-5-(hexylsulfanyl)-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}phenyl)prop-2-yn-1-yl]propanamide × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8UVP Human p97/VCP R155H mutant structure with a triazole inhibitor (NSC819701/up) Deposited 2023-11-03	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	ADP ADENOSINE-5'-DIPHOSPHATE × 12 XO8 2-[(4P)-4-(4-{[(4P)-5-(cyclohexylsulfanyl)-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}-2,5-difluorophenyl)-2H-1,2,3-triazol-2-yl]-1-[(2R,6S)-2,6-dimethylmorpholin-4-yl]ethan-1-one × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8UVQ Human p97/VCP R155H mutant structure with a triazole inhibitor (NSC819701/down) Deposited 2023-11-03	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H Mutation：R155H	ADP ADENOSINE-5'-DIPHOSPHATE × 12 XO8 2-[(4P)-4-(4-{[(4P)-5-(cyclohexylsulfanyl)-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}-2,5-difluorophenyl)-2H-1,2,3-triazol-2-yl]-1-[(2R,6S)-2,6-dimethylmorpholin-4-yl]ethan-1-one × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
8VKU Structure of VCP in complex with an ATPase activator (D2 domains only, hexameric form) Deposited 2024-01-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	A1AC1 (3R)-N-[2-(ethylsulfanyl)phenyl]-3-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)butanamide × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM K.HEPES pH 7.5, 25 mM KCl, 2.5 mM MgCl2, 2.5 mM GSH, 0.5% DMSO, 0.01% FOM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8VLS Structure of VCP in complex with an ATPase activator (D2 domains only, dodecameric form) Deposited 2024-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	A1AC1 (3R)-N-[2-(ethylsulfanyl)phenyl]-3-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)butanamide × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM K.HEPES pH 7.5, 25 mM KCl, 2.5 mM MgCl2, 2.5 mM GSH, 0.5% DMSO, 0.01% FOM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8VOV Structure of VCP in complex with an ATPase activator and ADP (D2 domains only, hexameric form) Deposited 2024-01-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 A1AC1 (3R)-N-[2-(ethylsulfanyl)phenyl]-3-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)butanamide × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM K.HEPES pH 7.5, 25 mM KCl, 2.5 mM MgCl2, 2.5 mM GSH, 0.5% DMSO, 0.01% FOM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8YKA Cryo-EM structure of P97-VCPIP1 complex Deposited 2024-03-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 12–775（764 aa） Chain B 12–775（764 aa） Chain C 12–775（764 aa） Chain D 12–775（764 aa） Chain E 12–775（764 aa） Chain F 12–775（764 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9BOQ Human p97/VCP structure with a triazole inhibitor (NSC799462/dodecamer) Deposited 2024-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 24 XKM 3-(2,6-difluoro-4-{[(4P)-5-{[(2S)-hexan-2-yl]sulfanyl}-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}phenyl)prop-2-yn-1-yl (1-methylpiperidin-4-yl)carbamate × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9DIL Cryo-EM structure of VCP/p97 in complex with VCPIP1 (VCIP135) Deposited 2024-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–806（806 aa） Chain B 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9LLK The cryo-EM structure of the heterododecameric human Derlin-1/p97 complex Deposited 2025-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 21–806（786 aa） Chain B 21–806（786 aa） Chain C 21–806（786 aa） Chain D 21–806（786 aa） Chain E 21–806（786 aa） Chain F 21–806（786 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
9MPQ Cryo-EM structure of VCP (consensus) Deposited 2024-12-31	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9MPS Cryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (with extra D2 domain) Deposited 2024-12-31	Different construct Different mutation/modification Different oligomeric state	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9MPT Cryo-EM structure of VCPIP1 UBX domain bound to VCP N-domain (with D1 domain) Deposited 2024-12-31	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9MPU Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain) Deposited 2024-12-31	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9MPV Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP Deposited 2024-12-31	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9MQ6 Cryo-EM structure of VCP/p97 and VCPIP1 (VCIP135) in the presence of AMPPNP Deposited 2025-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–806（806 aa） Chain B 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9OHN Cryo-EM structure of human p97/VCP bound to inhibitor GND-135 Deposited 2025-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 2–806（805 aa） Chain B 2–806（805 aa） Chain C 2–806（805 aa） Chain D 2–806（805 aa） Chain E 2–806（805 aa） Chain F 2–806（805 aa） Chain G 2–806（805 aa） Chain H 2–806（805 aa） Chain I 2–806（805 aa） Chain J 2–806（805 aa） Chain K 2–806（805 aa） Chain L 2–806（805 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 A1CBF (1P)-1-{4-(benzylamino)-2-methyl-1-[2-(morpholin-4-yl)-2-oxoethyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-2-methyl-1H-indole-4-carboxamide × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.46 Å
9Y03 Cryo-EM structure of human VCP/p97-R89W mutant bound to ADP Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
9Y04 Cryo-EM structure of human VCP/p97-R89W mutant bound to ATPgammaS Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
9Y05 Cryo-EM structure of human VCP/p97-R89W mutant bound to CB-5083 Deposited 2025-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W Mutation：R89W	JDP 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
9Y06 Cryo-EM structure of human VCP/p97-T122P mutant bound to ADP Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：T122P Mutation：T122P Mutation：T122P Mutation：T122P Mutation：T122P Mutation：T122P	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
9Y07 Cryo-EM structure of human VCP/p97-T122P mutant bound to ATPgammaS Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：T122P Mutation：T122P Mutation：T122P Mutation：T122P Mutation：T122P Mutation：T122P	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.41 Å
9Y08 Cryo-EM structure of human VCP/p97-G128D mutant bound to ADP Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：G128D Mutation：G128D Mutation：G128D Mutation：G128D Mutation：G128D Mutation：G128D	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9Y09 Cryo-EM structure of human VCP/p97-G128D mutant bound to ATPgS Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：G128D Mutation：G128D Mutation：G128D Mutation：G128D Mutation：G128D Mutation：G128D	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
9Y0B Cryo-EM structure of human VCP/p97-G156D mutant bound to ADP Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：G156D Mutation：G156D Mutation：G156D Mutation：G156D Mutation：G156D Mutation：G156D	ADP ADENOSINE-5'-DIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9Y0C Cryo-EM structure of human VCP/p97-G156D mutant bound to ATPgammaS Deposited 2025-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Mutation：G156D Mutation：G156D Mutation：G156D Mutation：G156D Mutation：G156D Mutation：G156D	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9YP6 Structure of human VCP/p97 hexamer bound to ADP and UTE-156 Deposited 2025-10-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 A1CYL N-(3-{[(6P)-2-(methanesulfonyl)-6-(1-methyl-1H-pyrazol-4-yl)pyrimidin-4-yl]amino}phenyl)prop-2-enamide × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM HEPES-KOH pH 7.4, 100 mM KOAc, 10mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9YP8 Structure of human VCP/p97 dodecamer bound to ADP and UTE-156 Deposited 2025-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa） Chain G 1–806（806 aa） Chain H 1–806（806 aa） Chain I 1–806（806 aa） Chain J 1–806（806 aa） Chain K 1–806（806 aa） Chain L 1–806（806 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 A1CYL N-(3-{[(6P)-2-(methanesulfonyl)-6-(1-methyl-1H-pyrazol-4-yl)pyrimidin-4-yl]amino}phenyl)prop-2-enamide × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM HEPES-KOH pH 7.4, 100 mM KOAc, 10mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
9YRC p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2025-10-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–806（806 aa） Chain B 1–806（806 aa） Chain C 1–806（806 aa） Chain D 1–806（806 aa） Chain E 1–806（806 aa） Chain F 1–806（806 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9YW2 Complex structure of human p97 bound to Faf1 and Ufd1 (NTD focused) Deposited 2025-10-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–806（806 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å

143 other PDB entries and 156 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TERA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 27–832； UniProt 1–806 Author chain B； PDBConstruct 27–832； UniProt 1–806 Author chain C； PDBConstruct 27–832； UniProt 1–806 Author chain D； PDBConstruct 27–832； UniProt 1–806 Author chain E； PDBConstruct 27–832； UniProt 1–806 Author chain F； PDBConstruct 27–832； UniProt 1–806

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9mpr
Deposition date deposition_date	2024-12-31
最后修订 last_revision	2025-10-15
Structure title title	Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP
Keywords keywords	;double-ring hexameric complex, valosin containing protein, ATPase, VCP, mammalian, DUB, deubiquitinase, deubiquitinating enzyme, VCIP135, p97, VCPIP1, hydrolase, VCPID ;; HYDROLASE
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	47.03 Å
Radius of gyration Rg (electron density) rg_electron	46.07 Å
Forward intensity I(0) i0	2264770000.00
Molecular weight molecular_weight	396820.0 kDa
Excluded volume excluded_volume	497220 Å³
Envelope volume envelope_volume	680760 Å³
Hydration-shell volume shell_volume	114940 Å³
Envelope diameter envelope_diameter	158.4 Å
Shell Rg shell_rg	56.76 Å
Envelope Rg envelope_rg	45.07 Å
Shape Rg shape_rg	46.08 Å
Total Rg total_rg	46.43 Å
Total atoms total_atoms	55729
Residues n_residues	3563
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	148.3 Å
Rg (real space) rg_real	46.62 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	2.2650e+09
I(0) uncertainty (real space) i0_real_error	4.1220e+07
Rg (reciprocal space) rg_reciprocal	47.03 Å
I(0) (reciprocal space) i0_reciprocal	2266000000.0000
Solution quality estimate total_estimate	0.8812
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	143.9 Å
Skewness Skewness skewness	0.062
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	852600000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.951

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Deubiquitinating protein VCPIP1
Molecular weight formula_weight	137335.4 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I
Atom count atom_count	55729

MGDWSHPQFEKSGGGSGGLEVLFQGPGSMSQPPPPPPPLPPPPPPPEAPQTPSSLASAAASGGLLKRRDRRILSGSCPDPKCQARLFFPASGSVSIECTECGQRHEQQQLLGVEEVTDPDVVLHNLLRNALLGVTGAPKKNTELVKVMGLSNYHCKLLSPILARYGMDKQTGRAKLLRDMNQGELFDCALLGDRAFLIEPEHVNTVGYGKDRSGSLLYLHDTLEDIKRANKSQECLIPVHVDGDGHCLVHAVSRALVGRELFWHALRENLKQHFQQHLARYQALFHDFIDAAEWEDIINECDPLFVPPEGVPLGLRNIHIFGLANVLHRPIILLDSLSGMRSSGDYSATFLPGLIPAEKCTGKDGHLNKPICIAWSSSGRNHYIPLVGIKGAALPKLPMNLLPKAWGVPQDLIKKYIKLEEDGGCVIGGDRSLQDKYLLRLVAAMEEVFMDKHGIHPSLVADVHQYFYRRTGVIGVQPEEVTAAAKKAVMDNRLHKCLLCGALSELHVPPEWLAPGGKLYNLAKSTHGQLRTDKNYSFPLNNLVCSYDSVKDVLVPDYGMSNLTACNWCHGTSVRKVRGDGSIVYLDGDRTNSRSTGGKCGCGFKHFWDGKEYDNLPEAFPITLEWGGRVVRETVYWFQYESDSSLNSNVYDVAMKLVTKHFPGEFGSEILVQKVVHTILHQTAKKNPDDYTPVNIDGAHAQRVGDVQGQESESQLPTKIILTGQKTKTLHKEELNMSKTERTIQQNITEQASVMQKRKTEKLKQEQKGQPRTVSPSTIRDGPSSAPATPTKAPYSPTTSKEKKIRITTNDGRQSMVTLKSSTTFFELQESIAREFNIPPYLQCIRYGFPPKELMPPQAGMEKEPVPLQHGDRITIEILKSKAEGGQSAAAHSAHTVKQEDIAVTGKLSSKELQEQAEKEMYSLCLLATLMGEDVWSYAKGLPHMFQQGGVFYSIMKKTMGMADGKHCTFPHLPGKTFVYNASEDRLELCVDAAGHFPIGPDVEDLVKEAVSQVRAEATTRSRESSPSHGLLKLGSGGVVKKKSEQLHNVTAFQGKGHSLGTASGNPHLDPRARETSVVRKHNTGTDFSNSSTKTEPSVFTASSSNSELIRIAPGVVTMRDGRQLDPDLVEAQRKKLQEMVSSIQASMDRHLRDQSTEQSPSDLPQRKTEVVSSSAKSGSLQTGLPESFPLTGGTENLNTETTDGCVADALGAAFATRSKAQRGNSVEELEEMDSQDAEMTNTTEPMDHS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Transitional endoplasmic reticulum ATPase
Molecular weight formula_weight	92022.5 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

MGDYKDDDDKGGGSGGLEVLFQGPGSMASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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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	triclinic

Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	107859

fit	/app/data/saxs_computation/mp/9mpr/9mpr.fit
pddf	/app/data/pr_computation/mp/9mpr/9mpr.pr.out
profile	/app/data/saxs_computation/mp/9mpr/9mpr.dat

Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP

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

Deubiquitinating protein VCPIP1

State in the Current Structure

Other States of the Same Protein in the Database

Transitional endoplasmic reticulum ATPase

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)