3j94

Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy

Method: ELECTRON MICROSCOPY D_max: 140.5 Å Quality: GOOD

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

Vesicle-fusing ATPase

Cricetulus griseus

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–744 Chain B； UniProt 1–744 Chain C； UniProt 1–744 Chain D； UniProt 1–744 Chain E； UniProt 1–744 Chain F； UniProt 1–744	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer：50 mM Tris-Cl, 150 mM NaCl, 1 mM EDTA, 1 mM ATP, 1 mM DTT, 0.05% v/v Nonident P-40；pH 8；50 mM Tris-Cl, 150 mM NaCl, 1 mM EDTA, 1 mM ATP, 1 mM DTT, 0.05% v/v Nonident P-40 cryo-EM vitrification conditions：Blot for 3.5 seconds before plunging；90 K；Cryogen ETHANE；Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 4.20 Å R-free 0.302

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 3J94	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2N D2 DOMAIN OF N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN Deposited 1998-06-30	Different construct Different mutation/modification 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 477–740（264 aa） Fragment：D2	Not recorded	MG MAGNESIUM ION × 6 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；293 K；3-8% PEG 3350, 300 MM KCL, 100 MM TRIS-HCL, PH 8.0, 5 MM MGCL2, 5 MM GDCL3, 2 MM DTT, 2 MM AMP-PNP, temperature 293K	Resolution 1.75 Å R-free 0.223
1NSF D2 HEXAMERIZATION DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) Deposited 1998-06-26	Different construct Different mutation/modification 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 478–744（267 aa） Fragment：D2 HEXAMERIZATION DOMAIN	Not recorded	MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.05；pH 6.05	Resolution 1.90 Å R-free 0.244
1QCS N-TERMINAL DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) Deposited 1999-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa） Fragment：N-TERMINAL DOMAIN OF NSF	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；Vapor diffusion, hanging drop, 100 mM Tris pH 8.7, 2.0 M ammonium sulfate, 10 mM dithiothreitol (DTT), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.242
1QDN AMINO TERMINAL DOMAIN OF THE N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF) Deposited 1999-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–203（203 aa） Fragment：AMINO TERMINAL DOMAIN Chain B 1–203（203 aa） Fragment：AMINO TERMINAL DOMAIN Chain C 1–203（203 aa） Fragment：AMINO TERMINAL DOMAIN	Not recorded	SO4 SULFATE ION × 8 BME BETA-MERCAPTOETHANOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；TRIS, AMMONIUM SULPHATE, 2- MERCAPTOETHANOL, pH 8.2	Resolution 2.30 Å R-free 0.260
1QDN AMINO TERMINAL DOMAIN OF THE N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF) Deposited 1999-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–203（203 aa） Fragment：AMINO TERMINAL DOMAIN Chain B 1–203（203 aa） Fragment：AMINO TERMINAL DOMAIN Chain C 1–203（203 aa） Fragment：AMINO TERMINAL DOMAIN	Not recorded	SO4 SULFATE ION × 16 BME BETA-MERCAPTOETHANOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；TRIS, AMMONIUM SULPHATE, 2- MERCAPTOETHANOL, pH 8.2	Resolution 2.30 Å R-free 0.260
3J95 Structure of ADP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy Deposited 2014-12-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-Cl, 150 mM NaCl, 1 mM EDTA, 1 mM ATP, 1 mM DTT, 0.05% v/v Nonident P-40；pH 8；50 mM Tris-Cl, 150 mM NaCl, 1 mM EDTA, 1 mM ATP, 1 mM DTT, 0.05% v/v Nonident P-40 cryo-EM vitrification conditions Blot for 3.5 seconds before plunging；90 K；Cryogen ETHANE；Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 7.60 Å R-free 0.265
3J96 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State I) Deposited 2014-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40；pH 8；50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40 cryo-EM vitrification conditions Blot for 3.5 seconds before plunging；90 K；Cryogen ETHANE；Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 7.60 Å R-free 0.303
3J97 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State II) Deposited 2014-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40；pH 8；50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40 cryo-EM vitrification conditions Blot for 3.5 seconds before plunging；90 K；Cryogen ETHANE；Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 7.80 Å R-free 0.311
3J98 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIa) Deposited 2014-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40；pH 8；50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40 cryo-EM vitrification conditions Blot for 3.5 seconds before plunging.；90 K；Cryogen ETHANE；Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 8.40 Å R-free 0.328
3J99 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIb) Deposited 2014-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40；pH 8；50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40 cryo-EM vitrification conditions Blot for 3.5 seconds before plunging.；77 K；Cryogen ETHANE；Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 8.20 Å R-free 0.304
6IP2 NSF-D1D2 part in the whole 20S complex Deposited 2018-11-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6MDM The 20S supercomplex engaging the SNAP-25 N-terminus (class 1) Deposited 2018-09-04	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 4.40 Å
6MDN The 20S supercomplex engaging the SNAP-25 N-terminus (class 2) Deposited 2018-09-04	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 1–723（723 aa） Chain B 1–723（723 aa） Chain C 1–723（723 aa） Chain D 1–723（723 aa） Chain E 1–723（723 aa） Chain F 1–723（723 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 4.40 Å
6MDO The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 1) Deposited 2018-09-04	Different construct 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 1–723（723 aa） Chain B 1–723（723 aa） Chain C 1–723（723 aa） Chain D 1–723（723 aa） Chain E 1–723（723 aa） Chain F 1–723（723 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 3.90 Å
6MDP The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 2) Deposited 2018-09-04	Different construct 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 1–723（723 aa） Chain B 1–723（723 aa） Chain C 1–723（723 aa） Chain D 1–723（723 aa） Chain E 1–723（723 aa） Chain F 1–723（723 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 3.80 Å
9NV9 NSF Mg2+ class 1 heptamer Deposited 2025-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa） Chain G 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9NVD NSF Mg2+ class 2 hexamer Deposited 2025-03-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
9OJR 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 3 Deposited 2025-05-08	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 11 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9OJU 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 4 Deposited 2025-05-08	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9OJZ 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 5 Deposited 2025-05-08	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9OK5 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 16 Deposited 2025-05-09	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 9 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9OKC 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 17 Deposited 2025-05-09	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 8 PO4 PHOSPHATE ION × 3 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
9OLJ 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 18 Deposited 2025-05-12	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 10 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9OLO 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 19 Deposited 2025-05-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 10 PO4 PHOSPHATE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
9OMQ NSF, substrate free, hydrolyzing, class 24 Deposited 2025-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 4 PO4 PHOSPHATE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.86 Å
9PAF 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 6 Deposited 2025-06-25	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9PAG 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 7 Deposited 2025-06-25	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
9PB9 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 8 Deposited 2025-06-26	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9PBA 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 9 Deposited 2025-06-26	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9PBF 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 10 Deposited 2025-06-26	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.01 Å
9PBV 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 11 Deposited 2025-06-26	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9PC3 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 12 Deposited 2025-06-26	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9PCX 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 14 Deposited 2025-06-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 PO4 PHOSPHATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.03 Å
9PCZ 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 15 Deposited 2025-06-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 10 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9PD1 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 20 Deposited 2025-06-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9PD8 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 21 Deposited 2025-06-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.23 Å
9PDB 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 22 Deposited 2025-06-30	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 PO4 PHOSPHATE ION × 3 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.83 Å
9PDD 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 29 Deposited 2025-06-30	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 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
9PF2 NSF, substrate free, hydrolyzing, class 25 Deposited 2025-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
9PFC NSF, substrate free, hydrolyzing, class 26 Deposited 2025-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 7 PO4 PHOSPHATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9PFF Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), non-hydrolyzing, class 27 Deposited 2025-07-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–744（744 aa） Chain B 1–744（744 aa） Chain C 1–744（744 aa） Chain D 1–744（744 aa） Chain E 1–744（744 aa） Chain F 1–744（744 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9PFG Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), 4:2:2 alphaSNAP-syntaxin-1a H3-SNAP-25 SN1 subcomplex local refinement, non-hydrolyzing, class 28 Deposited 2025-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain J 1–744（744 aa） Chain K 1–744（744 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å

41 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NSF_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–747； UniProt 1–744 Author chain B； PDBConstruct 4–747； UniProt 1–744 Author chain C； PDBConstruct 4–747； UniProt 1–744 Author chain D； PDBConstruct 4–747； UniProt 1–744 Author chain E； PDBConstruct 4–747； UniProt 1–744 Author chain F； PDBConstruct 4–747； UniProt 1–744

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j94
Deposition date deposition_date	2014-12-05
Structure title title	Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy
Keywords keywords	ATPases associated with diverse cellular activities, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	46.47 Å
Radius of gyration Rg (electron density) rg_electron	45.54 Å
Forward intensity I(0) i0	1382010000.00
Molecular weight molecular_weight	306400.0 kDa
Excluded volume excluded_volume	383160 Å³
Envelope volume envelope_volume	580290 Å³
Hydration-shell volume shell_volume	101600 Å³
Envelope diameter envelope_diameter	142.2 Å
Shell Rg shell_rg	54.39 Å
Envelope Rg envelope_rg	43.99 Å
Shape Rg shape_rg	45.58 Å
Total Rg total_rg	45.77 Å
Total atoms total_atoms	21509
Residues n_residues	2895
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	140.5 Å
Rg (real space) rg_real	46.04 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.3820e+09
I(0) uncertainty (real space) i0_real_error	2.3010e+07
Rg (reciprocal space) rg_reciprocal	46.46 Å
I(0) (reciprocal space) i0_reciprocal	1383000000.0000
Solution quality estimate total_estimate	0.8885
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	62.0 Å
Skewness Skewness skewness	-0.019
Kurtosis Kurtosis kurtosis	-0.535
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	137900000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.885

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Vesicle-fusing ATPase
Molecular weight formula_weight	82907.4 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	21509

GAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFASRVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGESEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGHQLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLQVTRGDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEGASPLDFD

来源 Source

来源生物 organism	Cricetulus griseus
通用名 common_name	Chinese hamster
NCBI Class编号 ncbi_taxonomy_id	10029
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	11

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	311.194 Å
R factor r_factor	0.2819
R_work r_work	0.2808
R_free r_free	0.3023

Resolution resolution	4.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	50781

fit	/app/data/saxs_computation/j9/3j94/3j94.fit
pddf	/app/data/pr_computation/j9/3j94/3j94.pr.out
profile	/app/data/saxs_computation/j9/3j94/3j94.dat