← Back to search
3j98

Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIa)

Method: ELECTRON MICROSCOPY Dmax: 214.1 Å Quality: GOOD
▼

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

Vesicle-fusing ATPase

Cricetulus griseus

UniProt P18708

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 × 13 PDB declaration: tridecameric（13） 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 Alpha-soluble NSF attachment protein × 4 （P54921） Vesicle-associated membrane protein 2 × 1 （P63045） Syntaxin-1A × 1 （P32851） Synaptosomal-associated protein 25 × 1 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

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 3J98 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 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 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 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 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
3J99 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIb) Deposited 2014-12-05 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 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 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 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 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 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 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 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 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 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 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

Alpha-soluble NSF attachment protein

Rattus norvegicus

UniProt P54921

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 × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain G； UniProt 1–295 Chain H； UniProt 1–295 Chain I； UniProt 1–295 Chain J； UniProt 1–295 Not recorded Vesicle-fusing ATPase × 6 （P18708） Vesicle-associated membrane protein 2 × 1 （P63045） Syntaxin-1A × 1 （P32851） Synaptosomal-associated protein 25 × 1 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

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 3J98 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J96 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State I) Deposited 2014-12-05 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–295（295 aa）
Chain H 1–295（295 aa）
Chain I 1–295（295 aa）
Chain J 1–295（295 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–295（295 aa）
Chain H 1–295（295 aa）
Chain I 1–295（295 aa）
Chain J 1–295（295 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
3J99 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIb) Deposited 2014-12-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–295（295 aa）
Chain H 1–295（295 aa）
Chain I 1–295（295 aa）
Chain J 1–295（295 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
6MDM The 20S supercomplex engaging the SNAP-25 N-terminus (class 1) Deposited 2018-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–278（278 aa）
Chain L 1–278（278 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
9OJZ 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 5 Deposited 2025-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–295（295 aa）
Chain G 1–295（295 aa）
Chain H 1–295（295 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain K 1–295（295 aa）
Chain L 1–295（295 aa）
Chain M 1–295（295 aa）
Chain N 1–295（295 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–295（295 aa）
Chain F 1–295（295 aa）
Chain G 1–295（295 aa）
Chain H 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–295（295 aa）
Chain J 1–295（295 aa）
Chain K 1–295（295 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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
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 M 1–295（295 aa）
Chain N 1–295（295 aa）
Chain O 1–295（295 aa）
Chain P 1–295（295 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 K 1–295（295 aa）
Chain L 1–295（295 aa）
Chain M 1–295（295 aa）
Chain N 1–295（295 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
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 I 1–295（295 aa）
Chain J 1–295（295 aa）
Chain K 1–295（295 aa）
Chain L 1–295（295 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
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 L 1–295（295 aa）
Chain M 1–295（295 aa）
Chain N 1–295（295 aa）
Chain O 1–295（295 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 1–295（295 aa）
Chain F 1–295（295 aa）
Chain G 1–295（295 aa）
Chain H 1–295（295 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

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SNAA_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 3–297； UniProt 1–295 Author chain H； PDBConstruct 3–297； UniProt 1–295 Author chain I； PDBConstruct 3–297； UniProt 1–295 Author chain J； PDBConstruct 3–297； UniProt 1–295

Vesicle-associated membrane protein 2

Rattus norvegicus

UniProt P63045

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 × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain K； UniProt 28–89 Fragment：UNP residues 28-89 Vesicle-fusing ATPase × 6 （P18708） Alpha-soluble NSF attachment protein × 4 （P54921） Syntaxin-1A × 1 （P32851） Synaptosomal-associated protein 25 × 1 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

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 3J98 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1KIL Three-dimensional structure of the complexin/SNARE complex Deposited 2001-12-03 Different construct 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 A 28–92（65 aa） Fragment：SNARE motif (29-93)
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；27%(v/v) Iso-Propanol, 200mM MgCl2, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.305
1N7S High Resolution Structure of a Truncated Neuronal SNARE Complex Deposited 2002-11-16 Different construct 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 28–89（62 aa） Fragment：SBc
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 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 1–96（96 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 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 E 1–96（96 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 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 I 1–96（96 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
2KOG lipid-bound synaptobrevin solution NMR structure Deposited 2009-09-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–116（116 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；318 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 1 mM [U-99% 13C; U-99% 15N] synaptobrevin-1, 200 mM DPC-2, 20 mM MES-3, 150 mM NaCl-4, 5 mM DTT-5, 1 mM EDTA-6, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2N1T Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution Deposited 2015-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–93（69 aa） Fragment：UNP residues 25-93
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Pressure ambient
NMR sample composition 30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3HD7 HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1 Deposited 2009-05-07 Different construct 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 30–116（87 aa） Fragment：C-terminal fragment, UNP residues 30-116
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 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 E 30–116（87 aa） Fragment：C-terminal fragment, UNP residues 30-116
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–116（87 aa） Fragment：C-terminal fragment, UNP Residues 30-116
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 30–116（87 aa） Fragment：C-terminal fragment, UNP Residues 30-116
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
3J96 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State I) Deposited 2014-12-05 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain K 28–89（62 aa） Fragment：UNP residues 28-89
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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain K 28–89（62 aa） Fragment：UNP residues 28-89
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
3J99 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIb) Deposited 2014-12-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain K 28–89（62 aa） Fragment：UNP residues 28-89
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
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 28–89（62 aa） Fragment：UNP residues 28-89
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 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 G 28–89（62 aa） Fragment：UNP residues 28-89
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 28–89（62 aa） Fragment：UNP residues 28-89
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 28–89（62 aa） Fragment：UNP residues 28-89
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
5W5C Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex Deposited 2017-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 28–66（39 aa） Fragment：UNP residues 29-66
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 28–66（39 aa） Fragment：UNP residues 29-66
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
6A30 Crystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxtamembrane Linker Region Deposited 2018-06-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 87–92（6 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；PEG 3350, magnesium nitrate, 2-(N-Morpholino)ethanesulfonic acid (MES)
Resolution 2.79 Å R-free 0.239
6IP1 alpha-SNAP-SNARE subcomplex in the whole 20S complex Deposited 2018-11-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–94（94 aa） Fragment：UNP residues 1-94
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 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 J 1–89（89 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 J 1–72（72 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
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 A 28–89（62 aa） Fragment：residues 28-89
Chain E 28–89（62 aa） Fragment：residues 28-89
Chain I 28–89（62 aa） Fragment：residues 28-89
Chain M 28–89（62 aa） Fragment：residues 28-89
Chain Q 28–89（62 aa） Fragment：residues 28-89
Chain U 28–89（62 aa） Fragment：residues 28-89
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 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 28–89（62 aa）
Not recorded 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 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 E 28–89（62 aa）
Not recorded 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
7UDB Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2 Deposited 2022-03-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 29–83（55 aa）
Mutation：Q36C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

22 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VAMP2_RAT
Isoform —
PDB entities 3
Chains and sequence ranges Author chain K； PDBConstruct 2–63； UniProt 28–89

Syntaxin-1A

Rattus norvegicus

UniProt P32851

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 × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain L； UniProt 191–256 Fragment：UNP residues 191-256 Vesicle-fusing ATPase × 6 （P18708） Alpha-soluble NSF attachment protein × 4 （P54921） Vesicle-associated membrane protein 2 × 1 （P63045） Synaptosomal-associated protein 25 × 1 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

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 3J98 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BR0 THREE DIMENSIONAL STRUCTURE OF THE N-TERMINAL DOMAIN OF SYNTAXIN 1A Deposited 1998-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–146（120 aa） Fragment：N-TERMINAL
Mutation：C145S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；305 K；Ionic strength (raw mmCIF value) 60 mM phosphate；Pressure 1
Resolution not provided
1EZ3 CRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A Deposited 2000-05-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–150（127 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；PEG 1500, sodium acetate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Resolution 1.90 Å R-free 0.286
1EZ3 CRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A Deposited 2000-05-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–150（127 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；PEG 1500, sodium acetate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Resolution 1.90 Å R-free 0.286
1EZ3 CRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A Deposited 2000-05-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–150（127 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；PEG 1500, sodium acetate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Resolution 1.90 Å R-free 0.286
1HVV SELF-ASSOCIATION OF THE H3 REGION OF SYNTAXIN 1A: IMPLICATIONS FOR SNARE COMPLEX ASSEMBLY Deposited 2001-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 190–264（75 aa） Fragment：RESIDUES 190-264
Chain B 190–264（75 aa） Fragment：RESIDUES 190-264
Chain C 190–264（75 aa） Fragment：RESIDUES 190-264
Chain D 190–264（75 aa） Fragment：RESIDUES 190-264
Not recorded TAR D(-)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；sodium potassium tartrate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.273
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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 191–267（77 aa） Fragment：H3, SNARE motif
Chain D 191–267（77 aa） Fragment：H3, 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
1KIL Three-dimensional structure of the complexin/SNARE complex Deposited 2001-12-03 Different construct 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 B 192–250（59 aa） Fragment：SNARE motif (191-253)
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；27%(v/v) Iso-Propanol, 200mM MgCl2, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.305
1N7S High Resolution Structure of a Truncated Neuronal SNARE Complex Deposited 2002-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 191–256（66 aa） Fragment：SXc
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 180–262（83 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 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 F 180–262（83 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 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 J 180–262（83 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
1URQ Crystal structure of neuronal Q-SNAREs in complex with R-SNARE motif of Tomosyn Deposited 2003-10-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 188–259（72 aa） Fragment：T-SNARE COILED-COIL HOMOLOGY, RESIDUES 188-259
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；30% MPD, 50MM CACL2, 50MM MES PH 6.0
Resolution 2.00 Å R-free 0.225
2M8R Pre-Fusion Solution NMR Structure of Neuronal SNARE Syntaxin 1A Deposited 2013-05-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–288（106 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；313 K；Pressure ambient
NMR sample composition 1 mM [U-13C; U-15N; U-2H] syntaxin, 100 mM DPC, 10 mM HEPES, 10 mM MES, 10 mM sodium acetate, 150 mM sodium chloride, 5 mM DTT, 1 mM EDTA, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] syntaxin, 100 mM [U-99% 2H] DPC, 150 mM sodium chloride, 0.02 % sodium azide, 10 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2N1T Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution Deposited 2015-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 188–259（72 aa） Fragment：UNP residues 188-259
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Pressure ambient
NMR sample composition 30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3C98 Revised structure of the munc18a-syntaxin1 complex Deposited 2008-02-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–267（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；294 K；PEG400, Ammonium Acetate, Sodium Acetate, EDTA, 2-mercaptoethanol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.60 Å R-free 0.263
3HD7 HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1 Deposited 2009-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 183–288（106 aa） Fragment：C-terminal fragment, UNP residues 183-288
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 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 F 183–288（106 aa） Fragment：C-terminal fragment, UNP residues 183-288
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 183–288（106 aa） Fragment：C-terminal fragment, UNP Residues 183-288
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 183–288（106 aa） Fragment：C-terminal fragment, UNP Residues 183-288
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
3J96 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State I) Deposited 2014-12-05 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain L 191–256（66 aa） Fragment：UNP residues 191-256
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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain L 191–256（66 aa） Fragment：UNP residues 191-256
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
3J99 Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIb) Deposited 2014-12-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain L 191–256（66 aa） Fragment：UNP residues 191-256
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
3RK2 Truncated SNARE complex Deposited 2011-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.268
3RK2 Truncated SNARE complex Deposited 2011-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.268
3RK3 Truncated SNARE complex with complexin Deposited 2011-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.50 Å R-free 0.316
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain N 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain V 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain Z 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain d 191–253（63 aa） Fragment：UNP residues 191-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
4JEH Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex Deposited 2013-02-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–266（243 aa） Fragment：unp residues 24-266
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.223
4JEH Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex Deposited 2013-02-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 24–266（243 aa） Fragment：unp residues 24-266
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.223
4JEU Crystal Structure of Munc18a and Syntaxin1 with native N-terminus complex Deposited 2013-02-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–243（242 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.263
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 191–256（66 aa） Fragment：UNP residues 191-256
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 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 H 191–256（66 aa） Fragment：UNP residues 191-256
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 191–256（66 aa） Fragment：UNP residues 191-256
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 191–256（66 aa） Fragment：UNP residues 191-256
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 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 B 191–256（66 aa） Fragment：UNP residues 191-256
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 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 H 191–256（66 aa） Fragment：UNP residues 191-256
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 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 B 191–256（66 aa） Fragment：UNP residues 191-256
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 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 H 191–256（66 aa） Fragment：UNP residues 191-256
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
5W5C Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex Deposited 2017-06-14 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 B 191–256（66 aa） Fragment：UNP residues 191-256
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 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 B 191–256（66 aa） Fragment：UNP residues 191-256
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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 2–253（252 aa） Fragment：UNP residues 2-253
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 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 I 1–256（256 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 I 1–256（256 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
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 B 191–256（66 aa） Fragment：residues 191-256
Chain F 191–256（66 aa） Fragment：residues 191-256
Chain J 191–256（66 aa） Fragment：residues 191-256
Chain N 191–256（66 aa） Fragment：residues 191-256
Chain R 191–256（66 aa） Fragment：residues 191-256
Chain V 191–256（66 aa） Fragment：residues 191-256
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 191–256（66 aa）
Not recorded 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 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 F 191–256（66 aa）
Not recorded 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
7UDB Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2 Deposited 2022-03-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–253（252 aa）
Mutation：C145A,L165A,E166A,L205C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7UDC cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 Deposited 2022-03-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–253（252 aa）
Mutation：C145A, L165A, E166A, L205C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7XSJ The structure of the Mint1/Munc18-1/syntaxin-1 complex Deposited 2022-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 25–267（243 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2M Sodium Malonate, pH 7.0, 20% (v/v) PEG 3350
Resolution 3.20 Å R-free 0.270
9OJZ 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 5 Deposited 2025-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain H 1–267（267 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–267（267 aa）
Chain B 1–267（267 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 G 1–267（267 aa）
Chain H 1–267（267 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–267（267 aa）
Chain B 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain H 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain H 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain H 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain H 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain I 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain L 1–267（267 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–267（267 aa）
Chain H 1–267（267 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 G 1–267（267 aa）
Chain H 1–267（267 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 I 1–267（267 aa）
Chain J 1–267（267 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 G 1–267（267 aa）
Chain H 1–267（267 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 G 1–267（267 aa）
Chain H 1–267（267 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 H 191–267（77 aa）
Chain J 191–267（77 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 191–267（77 aa）
Chain D 191–267（77 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

53 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STX1A_RAT
Isoform —
PDB entities 4
Chains and sequence ranges Author chain L； PDBConstruct 2–67； UniProt 191–256

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

SAXS scattering curve SAXS Profile

SAXS profile for 3j98

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j98
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3j98
Deposition date deposition_date2014-12-05
Structure title titleStructure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIa)
Keywords keywordsvesicle trafficking, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier64.00 Å
Radius of gyration Rg (electron density) rg_electron63.66 Å
Forward intensity I(0) i04741300000.00
Molecular weight molecular_weight582930.0 kDa
Excluded volume excluded_volume730500 ų
Envelope volume envelope_volume1175000 ų
Hydration-shell volume shell_volume151660 ų
Envelope diameter envelope_diameter213.8 Å
Shell Rg shell_rg69.22 Å
Envelope Rg envelope_rg60.51 Å
Shape Rg shape_rg63.62 Å
Total Rg total_rg63.88 Å
Total atoms total_atoms40956
Residues n_residues5422
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax214.1 Å
Rg (real space) rg_real63.72 Å
Rg uncertainty (real space) rg_real_error1.55 Å
I(0) (real space) i0_real4.7410e+09
I(0) uncertainty (real space) i0_real_error8.6540e+07
Rg (reciprocal space) rg_reciprocal64.21 Å
I(0) (reciprocal space) i0_reciprocal4745000000.0000
Solution quality estimate total_estimate0.8615
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary80.3 Å
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.380
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha377100000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.708
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)