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11ve

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1)

Method: ELECTRON MICROSCOPY Dmax: 186.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear protein localization protein 4 homolog

Homo sapiens

UniProt Q8TAT6

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count Chain G； UniProt 1–608 Not recorded FAS-associated factor 1 × 2 （Q9UNN5） Ubiquitin recognition factor in ER-associated degradation protein 1 × 1 （Q92890） Transitional endoplasmic reticulum ATPase × 6 （P55072） 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

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 11VE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11SY Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused) Deposited 2026-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 2–608（607 aa）
Not recorded ZN ZINC ION × 2 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 4.28 Å
11TA Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused) Deposited 2026-03-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain G 2–608（607 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
7WWP Crystal structure of human Npl4 Deposited 2022-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 91–560（470 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M HEPES (pH6.5), 16 % (w/v) PEG 3350, and 5 % (v/v) MPD
Resolution 2.99 Å R-free 0.290
7WWQ Crystal structure of human Ufd1-Npl4 complex Deposited 2022-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 96–560（465 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M Tris-HCl (pH8.5), 5 % (v/v) glycerol, and 1.3 M magnesium sulfate hydrate
Resolution 2.72 Å R-free 0.277
9YRC p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2025-10-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–608（608 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPL4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain G； PDBConstruct 1–608； UniProt 1–608

FAS-associated factor 1

Homo sapiens

UniProt Q9UNN5

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count Chain M； UniProt 481–650 Chain O； UniProt 481–650 Not recorded Nuclear protein localization protein 4 homolog × 1 （Q8TAT6） Ubiquitin recognition factor in ER-associated degradation protein 1 × 1 （Q92890） Transitional endoplasmic reticulum ATPase × 6 （P55072） 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

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 11VE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11TA Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused) Deposited 2026-03-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain M 481–650（170 aa）
Chain O 481–650（170 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
1H8C UBX domain from human faf1 Deposited 2001-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–650（82 aa） Fragment：UBX DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；310 K
Resolution not provided
2DZM Solution Structure of the Ubiquitin-like Domain in Human FAS-associated factor 1 (hFAF1) Deposited 2006-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 99–191（93 aa） Fragment：ubiquitin-like domain, residues 8-100
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.17mM ubiquitin-like domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
Resolution not provided
2EC4 Solution structure of the UAS domain from human FAS-associated factor 1 Deposited 2007-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 325–495（171 aa） Fragment：UAS domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 0.78mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3E21 Crystal structure of FAF-1 UBA Domain Deposited 2008-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 5–47（43 aa） Fragment：Ubiquitin-associated Domain, UNP residues 5-47
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；25% PEG 3350, 0.2M ammonium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.73 Å R-free 0.222
3QC8 Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change Deposited 2011-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 571–650（80 aa） Fragment：UBX 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
3QCA Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change Deposited 2011-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 571–650（80 aa） Fragment：UBX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Ammonium Sulfate, 0.1M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.293
3QCA Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change Deposited 2011-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 571–650（80 aa） Fragment：UBX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Ammonium Sulfate, 0.1M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.293
3QCA Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change Deposited 2011-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 571–650（80 aa） Fragment：UBX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Ammonium Sulfate, 0.1M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.293
3QCA Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change Deposited 2011-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 571–650（80 aa） Fragment：UBX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Ammonium Sulfate, 0.1M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.293
3QQ8 Crystal structure of p97-N in complex with FAF1-UBX Deposited 2011-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 568–650（83 aa） Fragment：unp residues 568-650
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16-20% PEG MME 2000, 0.2 M Trimethyl-N-oxide, 0.1 M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.5
Resolution 2.00 Å R-free 0.210
3QWZ Crystal structure of FAF1 UBX-p97N-domain complex Deposited 2011-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 571–650（80 aa） Fragment：FAF1 UBX domain, UNP residues 571-650
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 571–650（80 aa） Fragment：FAF1 UBX domain, UNP residues 571-650
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
3QX1 Crystal structure of FAF1 UBX domain Deposited 2011-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 571–650（80 aa） Fragment：FAF1 UBX domain, UNP residues 571-650
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；30% PEG 3350, 0.2M Lithium sulfate, 0.1M HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.218
3QX1 Crystal structure of FAF1 UBX domain Deposited 2011-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 571–650（80 aa） Fragment：FAF1 UBX domain, UNP residues 571-650
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；30% PEG 3350, 0.2M Lithium sulfate, 0.1M HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.218
3R3M Crystal structure of the FAF1 UBX domain Deposited 2011-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 568–650（83 aa） Fragment：unp residues 568-650
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole, 0.2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.00 Å R-free 0.258
3R3M Crystal structure of the FAF1 UBX domain Deposited 2011-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 568–650（83 aa） Fragment：unp residues 568-650
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole, 0.2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.00 Å R-free 0.258
3R3M Crystal structure of the FAF1 UBX domain Deposited 2011-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 568–650（83 aa） Fragment：unp residues 568-650
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole, 0.2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.00 Å R-free 0.258
3R3M Crystal structure of the FAF1 UBX domain Deposited 2011-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 568–650（83 aa） Fragment：unp residues 568-650
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole, 0.2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.00 Å R-free 0.258
7FGM The complex crystals structure of the FAF1 UBL1_L-Hsp70 NBD with ADP and phosphate Deposited 2021-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 91–171（81 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM Imidazole-malate pH 8.5 12 % PEG 10,000
Resolution 2.20 Å R-free 0.206
7FGN The crystal structure of the FAF1 UBL1 Deposited 2021-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 100–174（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50 mM Bis-Tris pH 6.5 50 mM (NH4)2SO4 30 % v/v pentaerythritol ethoxylate
Resolution 1.20 Å R-free 0.245
8KG2 Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain Deposited 2023-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain M 575–650（76 aa）
Chain N 575–650（76 aa）
Chain O 575–650（76 aa）
Chain P 575–650（76 aa）
Chain Q 575–650（76 aa）
Chain R 575–650（76 aa）
Chain S 575–650（76 aa）
Chain T 575–650（76 aa）
Chain U 575–650（76 aa）
Chain V 575–650（76 aa）
Chain W 575–650（76 aa）
Chain X 575–650（76 aa）
Not recorded 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
9YW2 Complex structure of human p97 bound to Faf1 and Ufd1 (NTD focused) Deposited 2025-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–650（650 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

15 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FAF1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain M； PDBConstruct 4–173； UniProt 481–650 Author chain O； PDBConstruct 4–173； UniProt 481–650

Ubiquitin recognition factor in ER-associated degradation protein 1

Homo sapiens

UniProt Q92890

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count Chain P； UniProt 1–307 Not recorded Nuclear protein localization protein 4 homolog × 1 （Q8TAT6） FAS-associated factor 1 × 2 （Q9UNN5） Transitional endoplasmic reticulum ATPase × 6 （P55072） 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

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 11VE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11SY Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused) Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 1–307（307 aa）
Not recorded ZN ZINC ION × 2 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 4.28 Å
11TA Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused) Deposited 2026-03-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain P 1–307（307 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
5C1B p97-delta709-728 in complex with a UFD1-SHP peptide Deposited 2015-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 221–241（21 aa） Fragment：UNP residues 221-241
Chain V 221–241（21 aa） Fragment：UNP residues 221-241
Not recorded 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
7WWQ Crystal structure of human Ufd1-Npl4 complex Deposited 2022-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 258–273（16 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M Tris-HCl (pH8.5), 5 % (v/v) glycerol, and 1.3 M magnesium sulfate hydrate
Resolution 2.72 Å R-free 0.277
9YRC p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2025-10-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–307（307 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–307（307 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

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

View Construct and Data Evidence
UniProt name UFD1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain P； PDBConstruct 1–307； UniProt 1–307

Transitional endoplasmic reticulum ATPase

Homo sapiens

UniProt P55072

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count Chain A； UniProt 1–806 Chain B； UniProt 1–806 Chain C； UniProt 1–806 Chain D； UniProt 1–806 Chain E； UniProt 1–806 Chain F； UniProt 1–806 Not recorded Nuclear protein localization protein 4 homolog × 1 （Q8TAT6） FAS-associated factor 1 × 2 （Q9UNN5） Ubiquitin recognition factor in ER-associated degradation protein 1 × 1 （Q92890） 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

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

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

View Construct and Data Evidence
UniProt name TERA_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 1–806； UniProt 1–806 Author chain B； PDBConstruct 1–806； UniProt 1–806 Author chain C； PDBConstruct 1–806； UniProt 1–806 Author chain D； PDBConstruct 1–806； UniProt 1–806 Author chain E； PDBConstruct 1–806； UniProt 1–806 Author chain F； PDBConstruct 1–806； UniProt 1–806

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 11ve

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 11ve
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2. Structure Basics 2. Structure Basics

Entry ID entry_id11ve
Deposition date deposition_date2026-03-13
Structure title titleCryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1)
Keywords keywordsERAD, ubiquitin, AAA+ ATPase, unfoldase, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier56.58 Å
Radius of gyration Rg (electron density) rg_electron56.07 Å
Forward intensity I(0) i03789840000.00
Molecular weight molecular_weight503330.0 kDa
Excluded volume excluded_volume624450 ų
Envelope volume envelope_volume978050 ų
Hydration-shell volume shell_volume139730 ų
Envelope diameter envelope_diameter189.4 Å
Shell Rg shell_rg62.96 Å
Envelope Rg envelope_rg55.64 Å
Shape Rg shape_rg56.14 Å
Total Rg total_rg56.02 Å
Total atoms total_atoms35382
Residues n_residues4663
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax186.9 Å
Rg (real space) rg_real56.35 Å
Rg uncertainty (real space) rg_real_error1.44 Å
I(0) (real space) i0_real3.7900e+09
I(0) uncertainty (real space) i0_real_error7.6360e+07
Rg (reciprocal space) rg_reciprocal56.76 Å
I(0) (reciprocal space) i0_reciprocal3792000000.0000
Solution quality estimate total_estimate0.6403
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary73.4 Å
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.288
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha451100000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 0.041; Positv: 1.000; Valcen: 0.966; Smooth: 0.805
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)