5low

Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)

Method: X-RAY DIFFRACTION D_max: 173.7 Å Quality: GOOD

▼

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

Rabphilin-3A

Rattus norvegicus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 536–680 Chain B； UniProt 536–680 Chain C； UniProt 536–680	Not recorded	Synaptosomal-associated protein 25 × 2 （P60881） Synaptosomal-associated protein 25 × 2 （P60881） GOL GLYCEROL × 3 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain H； UniProt 536–680 Chain I； UniProt 536–680 Chain J； UniProt 536–680	Not recorded	Synaptosomal-associated protein 25 × 2 （P60881） Synaptosomal-associated protein 25 × 2 （P60881） GOL GLYCEROL × 4 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269

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 5LOW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZBD STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A Deposited 1998-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 41–170（130 aa） Fragment：40-170, EFFECTOR DOMAIN	Mutation：C108S Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.263
1ZBD STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A Deposited 1998-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 41–170（130 aa） Fragment：40-170, EFFECTOR DOMAIN	Mutation：C108S Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.263
2CHD Crystal structure of the C2A domain of Rabphilin-3A Deposited 2006-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 371–510（140 aa） Fragment：C2A DOMAIN, RESIDUES 371-510	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG4000, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH=4.6	Resolution 1.92 Å R-free 0.269
2CM5 crystal structure of the C2B domain of rabphilin Deposited 2006-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 519–684（166 aa） Fragment：C2B DOMAIN AND LINKER, RESIDUES 519-684	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1M HEPES PH 8.5,20 % PEG MME 2000 OR 20 % PEG 8000	Resolution 1.28 Å R-free 0.194
2CM6 crystal structure of the C2B domain of rabphilin3A Deposited 2006-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 519–684（166 aa） Fragment：C2B DOMAIN AND LINKER, RESIDUES 519-684	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M HEPES PH 7.6, 25 % PEG 8000, 200 MM CA	Resolution 1.85 Å R-free 0.268
2CM6 crystal structure of the C2B domain of rabphilin3A Deposited 2006-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 519–684（166 aa） Fragment：C2B DOMAIN AND LINKER, RESIDUES 519-684	Not recorded	CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M HEPES PH 7.6, 25 % PEG 8000, 200 MM CA	Resolution 1.85 Å R-free 0.268
3RPB THE C2B-DOMAIN OF RABPHILIN: STRUCTURAL VARIATIONS IN A JANUS-FACED DOMAIN Deposited 1999-04-19	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 541–680（140 aa） Fragment：C2B DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；304.5 K；Ionic strength (raw mmCIF value) 150 mM NMR sample composition 95% WATER/5% D2O	Resolution not provided
4LT7 Crystal structure of the c2a domain of rabphilin-3a in complex with a calcium Deposited 2013-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–510（133 aa） Fragment：C2 1 domain residues 378-510	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；10 mM CaCl2, 150mM NaCl, 25mM HEPES ph 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.289
4NP9 Structure of Rabphilin C2A domain bound to IP3 Deposited 2013-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–510（133 aa） Fragment：C2 domain, UNP RESIDUES 378-510	Not recorded	I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；25-28% PEG 4K, 10-20mM Ammonium sulfate, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.92 Å R-free 0.250
4NS0 The C2A domain of Rabphilin 3A in complex with PI(4,5)P2 Deposited 2013-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–510（133 aa） Fragment：C2 domain, UNP RESIDUES 378-510	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25mM Hepes, 20mM Ammonuim Sulphate, 25% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.226
5LO8 The C2B domain of Rabphilin 3A in complex with PI(4,5)P2 Deposited 2016-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 536–680（145 aa） Fragment：C2B domain, UNP Residues 536-680	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 1 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24% PEG3350 0.1M ammonium sulfate 50mM Tris pH 7.5	Resolution 2.50 Å R-free 0.265
5LO8 The C2B domain of Rabphilin 3A in complex with PI(4,5)P2 Deposited 2016-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 536–680（145 aa） Fragment：C2B domain, UNP Residues 536-680	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 3 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24% PEG3350 0.1M ammonium sulfate 50mM Tris pH 7.5	Resolution 2.50 Å R-free 0.265
5LOB Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group) Deposited 2016-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 536–680（145 aa） Chain B 536–680（145 aa） Chain C 536–680（145 aa）	Not recorded	CA CALCIUM ION × 6 SO4 SULFATE ION × 10 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris pH 8.5	Resolution 3.30 Å R-free 0.286

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RP3A_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–162； UniProt 536–680 Author chain B； PDBConstruct 18–162； UniProt 536–680 Author chain C； PDBConstruct 18–162； UniProt 536–680 Author chain H； PDBConstruct 18–162； UniProt 536–680 Author chain I； PDBConstruct 18–162； UniProt 536–680 Author chain J； PDBConstruct 18–162； UniProt 536–680

Synaptosomal-associated protein 25

Rattus norvegicus

UniProt P60881

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain D； UniProt 7–82 Chain E； UniProt 141–203 Chain F； UniProt 7–82 Chain G； UniProt 141–203	Not recorded	Rabphilin-3A × 3 （P47709） GOL GLYCEROL × 3 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain K； UniProt 7–82 Chain L； UniProt 141–203 Chain M； UniProt 7–82 Chain N； UniProt 141–203	Not recorded	Rabphilin-3A × 3 （P47709） GOL GLYCEROL × 4 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5LOW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JTH Crystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a Deposited 2001-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–82（82 aa） Fragment：N-terminal SNARE motif Chain C 1–82（82 aa） Fragment：N-terminal SNARE motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, temperature 294K	Resolution 2.00 Å R-free 0.289
1N7S High Resolution Structure of a Truncated Neuronal SNARE Complex Deposited 2002-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 7–83（77 aa） Fragment：SN1b Chain D 141–204（64 aa） Fragment：SN2c	Not recorded	CA CALCIUM ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, CaCl2, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K	Resolution 1.45 Å R-free 0.224
1SFC NEURONAL SYNAPTIC FUSION COMPLEX Deposited 1998-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–83（83 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT Chain D 120–206（87 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT	Not recorded	SR STRONTIUM ION × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL	Resolution 2.40 Å R-free 0.303
1SFC NEURONAL SYNAPTIC FUSION COMPLEX Deposited 1998-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–83（83 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT Chain H 120–206（87 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT	Not recorded	SR STRONTIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL	Resolution 2.40 Å R-free 0.303
1SFC NEURONAL SYNAPTIC FUSION COMPLEX Deposited 1998-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 1–83（83 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT Chain L 120–206（87 aa） Fragment：PROTEOLYTICALLY PROTECTED FRAGMENT	Not recorded	SR STRONTIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL	Resolution 2.40 Å R-free 0.303
3HD7 HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1 Deposited 2009-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 7–83（77 aa） Fragment：N-terminal fragment, UNP residues 7-83 Chain D 141–204（64 aa） Fragment：C-terminal fragment, UNP residues 141-204	Not recorded	GGG glycylglycylglycine × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；29% PEG 400, 0.1M HEPES, 0.2M lithium sulfate, 0.1M sodium chloride, 0.03M glycylglycylglycine, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.40 Å R-free 0.271
3HD7 HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1 Deposited 2009-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 7–83（77 aa） Fragment：N-terminal fragment, UNP residues 7-83 Chain H 141–204（64 aa） Fragment：C-terminal fragment, UNP residues 141-204	Not recorded	GGG glycylglycylglycine × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；29% PEG 400, 0.1M HEPES, 0.2M lithium sulfate, 0.1M sodium chloride, 0.03M glycylglycylglycine, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.40 Å R-free 0.271
3IPD Helical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21 Deposited 2009-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 7–83（77 aa） Fragment：N-terminal fragment, UNP Residues 7-83 Chain D 141–204（64 aa） Fragment：C-terminal fragment, UNP Residues 141-204	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；16% MPD, 0.1M TRIS, 0.05M MAGNESIUM CHLORIDE, 3% SORBITOL, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 4.80 Å R-free 0.332
3IPD Helical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21 Deposited 2009-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 7–83（77 aa） Fragment：N-terminal fragment, UNP Residues 7-83 Chain H 141–204（64 aa） Fragment：C-terminal fragment, UNP Residues 141-204	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；16% MPD, 0.1M TRIS, 0.05M MAGNESIUM CHLORIDE, 3% SORBITOL, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 4.80 Å R-free 0.332
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.352
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 7–83（77 aa） Fragment：UNP residues 7-83 Chain J 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.352
5CCH Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.60 Å R-free 0.289
5CCI Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.75% v/v PEG3350, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2	Resolution 4.10 Å R-free 0.323
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction Deposited 2016-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 9–83（75 aa） Fragment：UNP residues 9-83 Chain D 141–204（64 aa） Fragment：UNP residues 141- 204	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction Deposited 2016-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 9–83（75 aa） Fragment：UNP residues 9-83 Chain J 141–204（64 aa） Fragment：UNP residues 141- 204	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction Deposited 2016-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 9–83（75 aa） Fragment：UNP residues 9-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction Deposited 2016-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 9–83（75 aa） Fragment：UNP residues 9-83 Chain J 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5LOB Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group) Deposited 2016-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 7–82（76 aa） Fragment：N-terminal helix Chain E 141–203（63 aa） Fragment：C-terminal helix Chain F 7–82（76 aa） Fragment：N-terminal helix Chain G 141–203（63 aa） Fragment：C-terminal helix	Not recorded	CA CALCIUM ION × 6 SO4 SULFATE ION × 10 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris pH 8.5	Resolution 3.30 Å R-free 0.286
5W5C Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex Deposited 2017-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	MG MAGNESIUM ION × 2 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM HEPES, pH7.4, 15-20% PEG3350, 200 mM ammonium formate	Resolution 1.85 Å R-free 0.232
5W5D Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex Deposited 2017-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 7–83（77 aa） Fragment：UNP residues 7-83 Chain D 141–204（64 aa） Fragment：UNP residues 141-204	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM HEPES, pH7.0, 15-17% PEG3350, 240 mM sodium malonate	Resolution 2.50 Å R-free 0.231
6IP1 alpha-SNAP-SNARE subcomplex in the whole 20S complex Deposited 2018-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–100（100 aa） Fragment：UNP residues 1-100 Chain D 126–206（81 aa） Fragment：UNP residues 126-206	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6MDM The 20S supercomplex engaging the SNAP-25 N-terminus (class 1) Deposited 2018-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–204（204 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 4.40 Å
6MDN The 20S supercomplex engaging the SNAP-25 N-terminus (class 2) Deposited 2018-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain H 1–204（204 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 4.40 Å
6MDO The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 1) Deposited 2018-09-04	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–204（204 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging.	Resolution 3.90 Å
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 mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–204（204 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain C 7–83（77 aa） Fragment：residues 7-83 Chain D 141–204（64 aa） Fragment：residues 141-204 Chain G 7–83（77 aa） Fragment：residues 7-83 Chain H 141–204（64 aa） Fragment：residues 141-204 Chain K 7–83（77 aa） Fragment：residues 7-83 Chain L 141–204（64 aa） Fragment：residues 141-204 Chain O 7–83（77 aa） Fragment：residues 7-83 Chain P 141–204（64 aa） Fragment：residues 141-204 Chain S 7–83（77 aa） Fragment：residues 7-83 Chain T 141–204（64 aa） Fragment：residues 141-204 Chain W 7–83（77 aa） Fragment：residues 7-83 Chain X 141–204（64 aa） Fragment：residues 141-204	Not recorded	MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.40 Å
6WVW Crystal structure of the R59P-SNAP25 containing SNARE complex Deposited 2020-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 10–83（74 aa） Chain D 141–204（64 aa）	Mutation：R59P	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM MES (pH 6.0), 100 mM CaCl2, 20-25% (v/v)	Resolution 2.11 Å R-free 0.244
6WVW Crystal structure of the R59P-SNAP25 containing SNARE complex Deposited 2020-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 10–83（74 aa） Chain H 141–204（64 aa）	Mutation：R59P	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM MES (pH 6.0), 100 mM CaCl2, 20-25% (v/v)	Resolution 2.11 Å R-free 0.244
9OJR 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 3 Deposited 2025-05-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–83（83 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 11 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9OJU 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 4 Deposited 2025-05-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–83（83 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9OJZ 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 5 Deposited 2025-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9OK3 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), 3:2:1 alphaSNAP-syntaxin-1a-SNAP-25 subcomplex local refinement, non-hydrolyzing, class 13 Deposited 2025-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–206（206 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
9OLO 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 19 Deposited 2025-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–206（206 aa） Chain J 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 10 PO4 PHOSPHATE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
9OM6 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), 4:2:2 alphaSNAP-syntaxin-1a-SNAP-25 subcomplex local refinement, hydrolyzing, class 23 Deposited 2025-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–206（206 aa） Chain D 1–206（206 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
9PAF 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 6 Deposited 2025-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–206（206 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9PAG 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 7 Deposited 2025-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
9PB9 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 8 Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9PBA 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 9 Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9PBF 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 10 Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–206（206 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.01 Å
9PBV 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 11 Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–206（206 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9PC3 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 12 Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9PCX 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 14 Deposited 2025-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–206（206 aa） Chain J 1–206（206 aa） Chain K 1–206（206 aa） Chain L 1–206（206 aa） Chain M 1–206（206 aa） Chain N 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 PO4 PHOSPHATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.03 Å
9PCZ 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 15 Deposited 2025-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain K 1–206（206 aa） Chain L 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 10 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9PD1 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 20 Deposited 2025-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–206（206 aa） Chain J 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9PD8 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 21 Deposited 2025-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain I 1–206（206 aa） Chain J 1–206（206 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.23 Å
9PFF Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), non-hydrolyzing, class 27 Deposited 2025-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain G 1–83（83 aa） Chain I 1–83（83 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9PFG Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), 4:2:2 alphaSNAP-syntaxin-1a H3-SNAP-25 SN1 subcomplex local refinement, non-hydrolyzing, class 28 Deposited 2025-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–83（83 aa） Chain C 1–83（83 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å

39 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNP25_RAT
Isoform	P60881-2
PDB entities	2, 3
Chains and sequence ranges	Author chain D； PDBConstruct 20–95； UniProt 7–82 Author chain F； PDBConstruct 20–95； UniProt 7–82 Author chain K； PDBConstruct 20–95； UniProt 7–82 Author chain M； PDBConstruct 20–95； UniProt 7–82 Author chain E； PDBConstruct 20–82； UniProt 141–203 Author chain G； PDBConstruct 20–82； UniProt 141–203 Author chain L； PDBConstruct 20–82； UniProt 141–203 Author chain N； PDBConstruct 20–82； UniProt 141–203

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5low
Deposition date deposition_date	2016-08-10
Structure title title	Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)
Keywords keywords	membrane fusion, calcium, C2 domain, exocytosis; EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	45.44 Å
Radius of gyration Rg (electron density) rg_electron	46.16 Å
Forward intensity I(0) i0	412267000.00
Molecular weight molecular_weight	160210.0 kDa
Excluded volume excluded_volume	198270 Å³
Envelope volume envelope_volume	296840 Å³
Hydration-shell volume shell_volume	57680 Å³
Envelope diameter envelope_diameter	189.1 Å
Shell Rg shell_rg	46.36 Å
Envelope Rg envelope_rg	45.82 Å
Shape Rg shape_rg	46.17 Å
Total Rg total_rg	46.15 Å
Total atoms total_atoms	11191
Residues n_residues	1373
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	173.7 Å
Rg (real space) rg_real	45.77 Å
Rg uncertainty (real space) rg_real_error	1.86 Å
I(0) (real space) i0_real	4.1230e+08
I(0) uncertainty (real space) i0_real_error	7.5440e+06
Rg (reciprocal space) rg_reciprocal	45.45 Å
I(0) (reciprocal space) i0_reciprocal	412100000.0000
Solution quality estimate total_estimate	0.8178
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.6 Å
Skewness Skewness skewness	0.600
Kurtosis Kurtosis kurtosis	0.397
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25220000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.903

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Rabphilin-3A
Molecular weight formula_weight	18579.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,H,I,J
Atom count atom_count	11297

HMASMTGGQQMGRGSDFGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Synaptosomal-associated protein 25
Molecular weight formula_weight	10841.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,K,M

GSHMASMTGGQQMGRGSEFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Synaptosomal-associated protein 25
Molecular weight formula_weight	9223.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,L,N

GSHMASMTGGQQMGRGSEFARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

▼

7. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d5lowa_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d5lowb_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d5lowc_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d5lowd1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lowd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5lowe_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lowf_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lowg1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lowg2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5lowh_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d5lowi_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d5lowj_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d5lowk1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lowk2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5lowl_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lowm_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lown1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d5lown2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (11 domains)

Domain ID domain_id	5lowA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	5lowB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	5lowC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	5lowE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	5lowF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	5lowG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	5lowH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	5lowI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	5lowJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	5lowL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	5lowN00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	60.080 Å
Unit-cell length b length_b	239.496 Å
Unit-cell length c length_c	71.487 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	45.030 Å
R factor r_factor	0.2394
R_work r_work	0.2379
R_free r_free	0.2686

Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)

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

Rabphilin-3A

State in the Current Structure

Other States of the Same Protein in the Database

Synaptosomal-associated protein 25

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (18 domains)

CATH v4.4 (11 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/lo/5low/5low.fit
pddf	/app/data/pr_computation/lo/5low/5low.pr.out
profile	/app/data/saxs_computation/lo/5low/5low.dat