Transitional endoplasmic reticulum ATPase
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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 21–196 | Fragment：N domain (Residues 21-185) | Ubiquitin thioesterase OTU1 × 1 （P43558） | 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 |
| 2 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 21–196 | Fragment：N domain (Residues 21-185) | Ubiquitin thioesterase OTU1 × 1 （P43558） | 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 |
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 4KDI | 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 method 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 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
1–806（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 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: 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 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 × 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 |
| 4KDL Crystal structure of p97/VCP N in complex with OTU1 UBXL Deposited 2013-04-25 | Different construct Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
1–481（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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 mutation/modification 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
1–481（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 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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 method 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 method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 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
1–806（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 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 × 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 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 × 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 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 × 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 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 × 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 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 × 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 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 × 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 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 × 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 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 × 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 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
1–806（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 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
1–806（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 experimental method Different experimental conditions 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 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 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 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
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 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 × 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 construct Different mutation/modification Different oligomeric state Different experimental method 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
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 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：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 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：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 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：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 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：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 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：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 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：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 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：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 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
1–806（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 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：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 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
1–806（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 method 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 method 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 method 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 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
1–806（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 method 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 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
1–806（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 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
1–806（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 experimental method 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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 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 × 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 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 × 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 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
1–806（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 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
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 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
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 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 × 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 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 × 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 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 × 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 ligand/ion 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 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 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 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
1–806（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 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
1–806（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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 method 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 | 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 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
1–806（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 mutation/modification Different oligomeric state Different experimental method 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 experimental method 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 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 method 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 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
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 construct Different mutation/modification Different oligomeric state Different experimental method 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
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9MPR Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP Deposited 2024-12-31 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions 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 2.90 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 Different experimental method Different experimental conditions Different structure-quality metrics | 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions 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 method 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 method 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 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
1–806（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 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
1–806（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 method 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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 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
1–806（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 method 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 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 × 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 oligomeric state Different experimental method 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 155 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | TERA_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 18–193； UniProt 21–196 Author chain B； PDBConstruct 18–193； UniProt 21–196 |
