4v11

Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84

Method: X-RAY DIFFRACTION D_max: 54.2 Å Quality: GOOD

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

SYNAPTOTAGMIN-1

HOMO SAPIENS

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 273–422	Fragment：C2B DOMAIN, UNP RESIDUES 273-422	SYNAPTIC VESICLE GLYCOPROTEIN 2A × 1 （Q7L0J3） CA CALCIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.1 M HEPES PH 7.5, 18 % PEG 3350, 0.05 M CACL2	Resolution 1.95 Å R-free 0.196

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 4V11	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K45 C2A domain of synaptototagmin I solution structure in the FGF-1-C2A binary complex: key component in the fibroblast growthfactor non-classical pathway Deposited 2008-05-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 141–268（128 aa） Fragment：UNP residues 141-268	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50mM (NH4)2SO4；Pressure ambient NMR sample composition 1.0mM [U-100% 13C; U-100% 15N] C2A, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K4A FGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway Deposited 2008-06-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 141–268（128 aa） Fragment：C2 domain, UNP residues 141-268	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50mM (NH4)2SO4；Pressure ambient NMR sample composition 1.2mM FGF-1-C2A; 100% D2O \| 100% D2O	Resolution not provided
2KI6 The FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion Deposited 2009-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 141–268（128 aa） Fragment：C2A domain Chain F 141–268（128 aa） Fragment：C2A domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1.0mM [U-100% 13C; U-100% 15N] C2A domain of Syt1-1, 1.0mM FGF1-2, 1.0mM S100A13-3, S100A13-4, 25mM sodium phosphate-5, 100mM sodium chloride-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LHA Solution structure of C2B with IP6 Deposited 2011-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 271–422（152 aa） Fragment：C2B domain, UNP residues 272-422	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] protein-1, 1.1 mM INOSITOL HEXAKISPHOSPHATE-2, 150 mM sodium chloride-3, 20 mM MES-4, 2 mM DTT-5, 2 mM Calcium Chloride-6, 90% H2O/10% D2O \| 90% H2O/10% 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 272–419（148 aa） Fragment：C2B domain (UNP residues 272-419)	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
2R83 Crystal structure analysis of human synaptotagmin 1 C2A-C2B Deposited 2007-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 141–422（282 aa） Fragment：C2A-C2B Chain B 141–422（282 aa） Fragment：C2A-C2B	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；3M NACL, 75 MM SODIUM ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 4.50	Resolution 2.70 Å R-free 0.253
3F00 Crystal Structure of Synaptotagmin I C2A domain with Cu(II) Deposited 2008-10-24	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 141–266（126 aa） Fragment：UNP residues 141-266	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.36 Å R-free 0.244
3F01 Crystal Structure of Synaptotagmin I C2A domain with Cu(II) Deposited 2008-10-24	Different construct 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 141–266（126 aa） Fragment：UNP residues 141-266	Not recorded	SO4 SULFATE ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K	Resolution 1.70 Å R-free 0.229
3F04 Crystal Structure of Synaptotagmin I C2A domain Deposited 2008-10-24	Different construct 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 141–266（126 aa） Fragment：UNP residues 141-266	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K	Resolution 1.35 Å R-free 0.224
3F05 Crystal Structure of Synaptotagmin I C2A domain with Mn(II) Deposited 2008-10-24	Different construct 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 141–266（126 aa） Fragment：UNP residues 141-266	Not recorded	SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K	Resolution 1.40 Å R-free 0.228
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 33–53（21 aa） Fragment：toxin binding site (unp residues 33-53)	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.65 Å R-free 0.220
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 33–53（21 aa） Fragment：toxin binding site (unp residues 33-53)	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.65 Å R-free 0.220
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 33–53（21 aa） Fragment：toxin binding site (unp residues 33-53)	Not recorded	SO4 SULFATE ION × 8 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.65 Å R-free 0.220
6G5F Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1 Deposited 2018-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 33–53（21 aa）	Not recorded	GOL GLYCEROL × 3 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；1.1 M sodium malonate dibasic monohydrate, HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003	Resolution 2.50 Å R-free 0.232
6G5K Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 Deposited 2018-03-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 33–53（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1	Resolution 2.00 Å R-free 0.235
6G5K Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 Deposited 2018-03-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 33 33–53（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1	Resolution 2.00 Å R-free 0.235
6QNS Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1a receptors Deposited 2019-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–53（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294.15 K；20% v/v PEG6000, 0.1 M MES pH 6.0, 0.2 M sodium chloride	Resolution 2.40 Å R-free 0.229
6TZ3 Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+ Deposited 2019-08-09	Different construct 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 272–422（151 aa） Fragment：C2B domain, residues 272-422	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2M Ammonium Sulfate, 30% PEG3350	Resolution 1.17 Å R-free 0.175
6U41 1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G) Deposited 2019-08-22	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 272–422（151 aa）	Mutation：D304G	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；2.0 M Ammonium Sulfate, 0.1 M Sodium Acetate	Resolution 1.70 Å R-free 0.178
6U4U 1.3 A structure of a pathogenic human Syt 1 C2B (I368T) Deposited 2019-08-26	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 272–422（151 aa）	Mutation：I368T	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.5 M Ammonium Sulfate, 0.1 M Sodium Acetate	Resolution 1.30 Å R-free 0.169
6U4W 1.4 A structure of a pathogenic human Syt 1 C2B (D366E) Deposited 2019-08-26	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 272–422（151 aa）	Mutation：D366E	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；1.6 M Ammonium Sulfate, 0.1 M Citrate	Resolution 1.40 Å R-free 0.211
6ZVN Botulinum neurotoxin B2 binding domain in complex with human synaptotagmin I Deposited 2020-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain BBB 33–53（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000	Resolution 2.50 Å R-free 0.283
7U4Q Human Synaptotagmin-1 C2A Y181F Ca2+ bound Deposited 2022-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 141–267（127 aa） Fragment：C2A domain Chain B 141–267（127 aa） Fragment：C2A domain	Mutation：Y181F Mutation：Y181F	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；100 mM HEPES, 2.3 M malonate	Resolution 1.56 Å R-free 0.189
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid	Resolution 2.75 Å R-free 0.298

21 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 273–422

SYNAPTIC VESICLE GLYCOPROTEIN 2A

OrganismNot specified

UniProt Q7L0J3

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 81–90	Fragment：UNP RESIDUES 81-90 Non-standard monomer：Yes (specific site not provided by mmCIF)	SYNAPTOTAGMIN-1 × 1 （P21579） CA CALCIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.1 M HEPES PH 7.5, 18 % PEG 3350, 0.05 M CACL2	Resolution 1.95 Å R-free 0.196

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4V11	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8JLC Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
8JLE Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 480–587（108 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
8JLF Cryo-EM structure of SV2A in complex with BoNT/A2 Hc Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8JLG Cryo-EM structure of SV2A in complex with BoNT/A2 Hc Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 480–590（111 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
8JLH Cryo-EM structure of SV2A dimer in complex with BoNT/A2 Hc and levetiracetam Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–742（741 aa） Chain C 2–742（741 aa）	Not recorded	UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8JLI Cryo-EM structure of SV2A dimer in complex levetiracetam Deposited 2023-06-02	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 × 2 PDB declaration: dimeric	Chain A 2–742（741 aa） Chain B 2–742（741 aa）	Not recorded	UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
8JS8 Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam Deposited 2023-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
8JS9 Cryo-EM structure of SV2A in complex with BoNT/A2 Hc Deposited 2023-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8K77 Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and brivaracetam Deposited 2023-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VLX (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8UO9 Structure of synaptic vesicle protein 2A in complex with a nanobody Deposited 2023-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 64–742（679 aa）	Not recorded	X49 (4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(4,4,4-trifluorobutyl)pyrrolidin-2-one × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 PS1 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE] × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
8UOA Structure of the synaptic vesicle protein 2A Luminal domain in complex with a nanobody Deposited 2023-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 64–742（679 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris pH 8.0, 0.02 mM LMNG, 0.020 mM CHS, 0.050mM GDN, and 1 micromolar of UCB-2500 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8YF0 Cryo-EM structure of human SV2A Deposited 2024-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–734（734 aa） Chain C 1–734（734 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.49 Å
8YF1 Cryo-EM structure of human SV2A in complex with Brivaracetam Deposited 2024-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–734（734 aa） Chain B 1–734（734 aa）	Not recorded	VLX (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9NTC Structure of Synaptic Vesicle Protein 2A Bound to Brivaracetam and UCB1244283 Deposited 2025-03-18	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 64–742（679 aa）	Not recorded	A1B1J (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide × 1 VLX (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide × 1 CLR CHOLESTEROL × 1 A1B1I (3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9PC9 Structure of Synaptic Vesicle Protein 2A Bound to UCB7361 Deposited 2025-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–742（742 aa）	Not recorded	A1CHN (4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(3,3,3-trifluoropropyl)pyrrolidin-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
9PCB Structure of Synaptic Vesicle Protein 2A Bound to UCB-J Deposited 2025-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 64–742（679 aa）	Not recorded	A1CCA (4R)-1-[(3-methylpyridin-4-yl)methyl]-4-(3,4,5-trifluorophenyl)pyrrolidin-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
9PRS Cryo-EM structure of human SV2A in complex with Levetiracetam and UCB1244283 Deposited 2025-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 139–742（604 aa）	Not recorded	UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1 A1B1J (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SV2A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–10； UniProt 81–90

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4v11
Deposition date deposition_date	2014-09-22
Structure title title	Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
Keywords keywords	SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.56 Å
Radius of gyration Rg (electron density) rg_electron	15.37 Å
Forward intensity I(0) i0	6299580.00
Molecular weight molecular_weight	18439.0 kDa
Excluded volume excluded_volume	23264 Å³
Envelope volume envelope_volume	26374 Å³
Hydration-shell volume shell_volume	14448 Å³
Envelope diameter envelope_diameter	55.4 Å
Shell Rg shell_rg	21.34 Å
Envelope Rg envelope_rg	15.81 Å
Shape Rg shape_rg	15.32 Å
Total Rg total_rg	16.64 Å
Total atoms total_atoms	1290
Residues n_residues	159
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	54.2 Å
Rg (real space) rg_real	16.46 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	6.3000e+06
I(0) uncertainty (real space) i0_real_error	8.2710e+04
Rg (reciprocal space) rg_reciprocal	16.47 Å
I(0) (reciprocal space) i0_reciprocal	6300000.0000
Solution quality estimate total_estimate	0.7954
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.195
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1375000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SYNAPTOTAGMIN-1
Molecular weight formula_weight	17095.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1443

KLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	SYNAPTIC VESICLE GLYCOPROTEIN 2A
Molecular weight formula_weight	1155.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SDATEGHDED

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4v11A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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8. Citations (1)

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Unit-cell length a length_a	46.049 Å
Unit-cell length b length_b	41.432 Å
Unit-cell length c length_c	48.014 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	31.279 Å
R factor r_factor	0.1534
R_work r_work	0.1512
R_free r_free	0.1956

fit	/app/data/saxs_computation/v1/4v11/4v11.fit
pddf	/app/data/pr_computation/v1/4v11/4v11.pr.out
profile	/app/data/saxs_computation/v1/4v11/4v11.dat

Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84

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

SYNAPTOTAGMIN-1

State in the Current Structure

Other States of the Same Protein in the Database

SYNAPTIC VESICLE GLYCOPROTEIN 2A

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)