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)

Method: ELECTRON MICROSCOPY D_max: 143.7 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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–723 Chain B； UniProt 1–723 Chain C； UniProt 1–723 Chain D； UniProt 1–723 Chain E； UniProt 1–723 Chain F； UniProt 1–723	Not recorded	Synaptosomal-associated protein 25 × 1 （P60881） 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

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 6MDP	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 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 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 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 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 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 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
3J94 Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy Deposited 2014-12-05	Different construct 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 1–744（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	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
3J95 Structure of ADP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy Deposited 2014-12-05	Different construct 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 1–744（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 construct 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 construct 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 construct 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 construct 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 construct 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 1–744（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 construct Different oligomeric state 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 oligomeric state 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 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
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 construct 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 1–744（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 construct 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 construct 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 1–744（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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 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 1–744（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 construct 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 1–744（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 construct 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 1–744（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 construct 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 25–747； UniProt 1–723 Author chain B； PDBConstruct 25–747； UniProt 1–723 Author chain C； PDBConstruct 25–747； UniProt 1–723 Author chain D； PDBConstruct 25–747； UniProt 1–723 Author chain E； PDBConstruct 25–747； UniProt 1–723 Author chain F； PDBConstruct 25–747； UniProt 1–723

Synaptosomal-associated protein 25

Rattus norvegicus

UniProt P60881

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain H； UniProt 1–204	Not recorded	Vesicle-fusing ATPase × 6 （P18708） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6MDP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JTH Crystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a Deposited 2001-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–82（82 aa） Fragment：N-terminal SNARE motif Chain C 1–82（82 aa） Fragment：N-terminal SNARE motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, temperature 294K	Resolution 2.00 Å R-free 0.289
1N7S High Resolution Structure of a Truncated Neuronal SNARE Complex Deposited 2002-11-16	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 × 4 PDB declaration: tetrameric	Chain C 7–83（77 aa） Fragment：SN1b Chain D 141–204（64 aa） Fragment：SN2c	Not recorded	CA CALCIUM ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, CaCl2, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K	Resolution 1.45 Å R-free 0.224
1SFC NEURONAL SYNAPTIC FUSION COMPLEX Deposited 1998-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–83（83 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT Chain D 120–206（87 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT	Not recorded	SR STRONTIUM ION × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL	Resolution 2.40 Å R-free 0.303
1SFC NEURONAL SYNAPTIC FUSION COMPLEX Deposited 1998-08-24	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 1–83（83 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT Chain H 120–206（87 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT	Not recorded	SR STRONTIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL	Resolution 2.40 Å R-free 0.303
1SFC NEURONAL SYNAPTIC FUSION COMPLEX Deposited 1998-08-24	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 × 4 PDB declaration: tetrameric	Chain K 1–83（83 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT Chain L 120–206（87 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT	Not recorded	SR STRONTIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL	Resolution 2.40 Å R-free 0.303
3HD7 HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1 Deposited 2009-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 7–83（77 aa） Fragment：N-terminal fragment, UNP residues 7-83 Chain D 141–204（64 aa） Fragment：C-terminal fragment, UNP residues 141-204	Not recorded	GGG glycylglycylglycine × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；29% PEG 400, 0.1M HEPES, 0.2M lithium sulfate, 0.1M sodium chloride, 0.03M glycylglycylglycine, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.40 Å R-free 0.271
3HD7 HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1 Deposited 2009-05-07	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 7–83（77 aa） Fragment：N-terminal fragment, UNP residues 7-83 Chain H 141–204（64 aa） Fragment：C-terminal fragment, UNP residues 141-204	Not recorded	GGG glycylglycylglycine × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；29% PEG 400, 0.1M HEPES, 0.2M lithium sulfate, 0.1M sodium chloride, 0.03M glycylglycylglycine, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.40 Å R-free 0.271
3IPD Helical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21 Deposited 2009-08-17	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 × 4 PDB declaration: tetrameric	Chain C 7–83（77 aa） Fragment：N-terminal fragment, UNP Residues 7-83 Chain D 141–204（64 aa） Fragment：C-terminal fragment, UNP Residues 141-204	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；16% MPD, 0.1M TRIS, 0.05M MAGNESIUM CHLORIDE, 3% SORBITOL, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 4.80 Å R-free 0.332
3IPD Helical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21 Deposited 2009-08-17	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 7–83（77 aa） Fragment：N-terminal fragment, UNP Residues 7-83 Chain H 141–204（64 aa） Fragment：C-terminal fragment, UNP Residues 141-204	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；16% MPD, 0.1M TRIS, 0.05M MAGNESIUM CHLORIDE, 3% SORBITOL, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 4.80 Å R-free 0.332
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.352
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02	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 × 5 PDB declaration: pentameric	Chain I 7–83（77 aa） Fragment：UNP residues 7-83 Chain J 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.352
5CCH Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.60 Å R-free 0.289
5CCI Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.75% v/v PEG3350, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2	Resolution 4.10 Å R-free 0.323
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction 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 × 5 PDB declaration: pentameric	Chain C 9–83（75 aa） Fragment：UNP residues 9-83 Chain D 141–204（64 aa） Fragment：UNP residues 141- 204	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction 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 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 9–83（75 aa） Fragment：UNP residues 9-83 Chain J 141–204（64 aa） Fragment：UNP residues 141- 204	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction 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 × 5 PDB declaration: pentameric	Chain C 9–83（75 aa） Fragment：UNP residues 9-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction 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 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 9–83（75 aa） Fragment：UNP residues 9-83 Chain J 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5LOB Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group) Deposited 2016-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 7–82（76 aa） Fragment：N-terminal helix Chain E 141–203（63 aa） Fragment：C-terminal helix Chain F 7–82（76 aa） Fragment：N-terminal helix Chain G 141–203（63 aa） Fragment：C-terminal helix	Not recorded	CA CALCIUM ION × 6 SO4 SULFATE ION × 10 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris pH 8.5	Resolution 3.30 Å R-free 0.286
5LOW Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group) Deposited 2016-08-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 7–82（76 aa） Chain E 141–203（63 aa） Chain F 7–82（76 aa） Chain G 141–203（63 aa）	Not recorded	GOL GLYCEROL × 3 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269
5LOW Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group) Deposited 2016-08-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 7–82（76 aa） Chain L 141–203（63 aa） Chain M 7–82（76 aa） Chain N 141–203（63 aa）	Not recorded	GOL GLYCEROL × 4 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269
5W5C Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex Deposited 2017-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	MG MAGNESIUM ION × 2 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM HEPES, pH7.4, 15-20% PEG3350, 200 mM ammonium formate	Resolution 1.85 Å R-free 0.232
5W5D Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex Deposited 2017-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM HEPES, pH7.0, 15-17% PEG3350, 240 mM sodium malonate	Resolution 2.50 Å R-free 0.231
6IP1 alpha-SNAP-SNARE subcomplex in the whole 20S complex Deposited 2018-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–100（100 aa） Fragment：UNP residues 1-100 Chain D 126–206（81 aa） Fragment：UNP residues 126-206	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6MDM The 20S supercomplex engaging the SNAP-25 N-terminus (class 1) Deposited 2018-09-04	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–204（204 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 oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–204（204 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–204（204 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
6MTI Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+ Deposited 2018-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain C 7–83（77 aa） Fragment：residues 7-83 Chain D 141–204（64 aa） Fragment：residues 141-204 Chain G 7–83（77 aa） Fragment：residues 7-83 Chain H 141–204（64 aa） Fragment：residues 141-204 Chain K 7–83（77 aa） Fragment：residues 7-83 Chain L 141–204（64 aa） Fragment：residues 141-204 Chain O 7–83（77 aa） Fragment：residues 7-83 Chain P 141–204（64 aa） Fragment：residues 141-204 Chain S 7–83（77 aa） Fragment：residues 7-83 Chain T 141–204（64 aa） Fragment：residues 141-204 Chain W 7–83（77 aa） Fragment：residues 7-83 Chain X 141–204（64 aa） Fragment：residues 141-204	Not recorded	MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.40 Å
6WVW Crystal structure of the R59P-SNAP25 containing SNARE complex Deposited 2020-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 10–83（74 aa） Chain D 141–204（64 aa）	Mutation：R59P	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM MES (pH 6.0), 100 mM CaCl2, 20-25% (v/v)	Resolution 2.11 Å R-free 0.244
6WVW Crystal structure of the R59P-SNAP25 containing SNARE complex Deposited 2020-05-07	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 10–83（74 aa） Chain H 141–204（64 aa）	Mutation：R59P	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM MES (pH 6.0), 100 mM CaCl2, 20-25% (v/v)	Resolution 2.11 Å R-free 0.244
9OJR 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 3 Deposited 2025-05-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–83（83 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–83（83 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 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 I 1–206（206 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
9OK3 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), 3:2:1 alphaSNAP-syntaxin-1a-SNAP-25 subcomplex local refinement, non-hydrolyzing, class 13 Deposited 2025-05-08	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 C 1–206（206 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
9OLO 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 19 Deposited 2025-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–206（206 aa） Chain J 1–206（206 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
9OM6 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), 4:2:2 alphaSNAP-syntaxin-1a-SNAP-25 subcomplex local refinement, hydrolyzing, class 23 Deposited 2025-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–206（206 aa） Chain D 1–206（206 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
9PAF 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 6 Deposited 2025-06-25	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 I 1–206（206 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 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 I 1–206（206 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 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 I 1–206（206 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 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 I 1–206（206 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 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 H 1–206（206 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 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 H 1–206（206 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 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 I 1–206（206 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–206（206 aa） Chain J 1–206（206 aa） Chain K 1–206（206 aa） Chain L 1–206（206 aa） Chain M 1–206（206 aa） Chain N 1–206（206 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain K 1–206（206 aa） Chain L 1–206（206 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–206（206 aa） Chain J 1–206（206 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain I 1–206（206 aa） Chain J 1–206（206 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
9PFF Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), non-hydrolyzing, class 27 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 × 14 PDB declaration: tetradecameric	Chain G 1–83（83 aa） Chain I 1–83（83 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 A 1–83（83 aa） Chain C 1–83（83 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

39 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNP25_RAT
Isoform	P60881-2
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 4–207； UniProt 1–204

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	6mdp
Deposition date deposition_date	2018-09-04
Structure title title	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)
Keywords keywords	SNARE, NSF, SNAP, ATPase, AAA, disassembly, synapse, membrane fusion, exocytosis, 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	46.34 Å
Radius of gyration Rg (electron density) rg_electron	45.60 Å
Forward intensity I(0) i0	1485690000.00
Molecular weight molecular_weight	320490.0 kDa
Excluded volume excluded_volume	402070 Å³
Envelope volume envelope_volume	569170 Å³
Hydration-shell volume shell_volume	98371 Å³
Envelope diameter envelope_diameter	145.3 Å
Shell Rg shell_rg	54.62 Å
Envelope Rg envelope_rg	44.82 Å
Shape Rg shape_rg	45.63 Å
Total Rg total_rg	45.81 Å
Total atoms total_atoms	45342
Residues n_residues	2832
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	143.7 Å
Rg (real space) rg_real	45.98 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.4860e+09
I(0) uncertainty (real space) i0_real_error	2.3800e+07
Rg (reciprocal space) rg_reciprocal	46.34 Å
I(0) (reciprocal space) i0_reciprocal	1486000000.0000
Solution quality estimate total_estimate	0.8904
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	59.2 Å
Skewness Skewness skewness	0.047
Kurtosis Kurtosis kurtosis	-0.532
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	145900000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.899

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vesicle-fusing ATPase
Molecular weight formula_weight	85509.2 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	45342

MGHHHHHHDYDIPTTENLYFQGAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFASRVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGESEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGHQLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIIASTKVEVDMEKAESLQVTRGDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEGASPLDFD

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 polymer

Description description	Synaptosomal-associated protein 25
Molecular weight formula_weight	23512.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MASMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLGKCCGLFICPCNKLKSSDAYKKAWGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	9

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6mdpF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6mdpF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

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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	triclinic

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	184555

fit	/app/data/saxs_computation/md/6mdp/6mdp.fit
pddf	/app/data/pr_computation/md/6mdp/6mdp.pr.out
profile	/app/data/saxs_computation/md/6mdp/6mdp.dat

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)

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

Vesicle-fusing ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Synaptosomal-associated protein 25

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)