SAXSdb — 4isq

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

Neurotoxin

Clostridium botulinum

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 864–1285	Fragment：Hc domain (unp residues 864-1285)	Synaptotagmin-1 × 1 （P21579） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 864–1285	Fragment：Hc domain (unp residues 864-1285)	Synaptotagmin-1 × 1 （P21579） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 864–1285	Fragment：Hc domain (unp residues 864-1285)	Synaptotagmin-1 × 1 （P21579） 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

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 4ISQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3N7L Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain Deposited 2010-05-27	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 862–1285（424 aa） Fragment：Receptor Binding Domain (UNP residues 862-1285)	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.1M MES pH 6.0, 5% PEG400, 1.8 M ammonium, 250 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.257
3N7M Crystal structure of W1252A mutant of HCR D/C VPI 5995 Deposited 2010-05-27	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 862–1285（424 aa） Fragment：Receptor Binding Domain (UNP residues 862-1285)	Mutation：W1252A	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M Hepes pH 7.5, 4% PEG400, 45% ammonium sulfate, 250mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.60 Å R-free 0.270
4FVV Crystal structure of HCR/D-Sa-GBL1/C Deposited 2012-06-29	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 862–1285（424 aa） Fragment：receptor binding domain, UNP residues 862-1285	Mutation：loop of KLGDDYWFN(1246-1254) mutated to RLGGDWYR	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；292 K；16% PEG5K-MME, 50 mM MgSO4, 0.1 M HEPPs buffer, pH 8.5, EVAPORATION, temperature 292K	Resolution 2.70 Å R-free 0.263
4FVV Crystal structure of HCR/D-Sa-GBL1/C Deposited 2012-06-29	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 862–1285（424 aa） Fragment：receptor binding domain, UNP residues 862-1285	Mutation：loop of KLGDDYWFN(1246-1254) mutated to RLGGDWYR	GOL GLYCEROL × 2 SIA N-acetyl-alpha-neuraminic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；292 K；16% PEG5K-MME, 50 mM MgSO4, 0.1 M HEPPs buffer, pH 8.5, EVAPORATION, temperature 292K	Resolution 2.70 Å R-free 0.263
4ISR Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II Deposited 2013-01-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 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 2.59 Å R-free 0.235
4ISR Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II Deposited 2013-01-17	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 5	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 2.59 Å R-free 0.235
4ISR Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II Deposited 2013-01-17	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 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 2.59 Å R-free 0.235

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9LBR1_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–431； UniProt 864–1285 Author chain B； PDBConstruct 10–431； UniProt 864–1285 Author chain C； PDBConstruct 10–431； UniProt 864–1285

Synaptotagmin-1

OrganismNot specified

UniProt P21579

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 F； UniProt 33–53	Fragment：toxin binding site (unp residues 33-53)	Neurotoxin × 1 （Q9LBR1） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 33–53	Fragment：toxin binding site (unp residues 33-53)	Neurotoxin × 1 （Q9LBR1） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 33–53	Fragment：toxin binding site (unp residues 33-53)	Neurotoxin × 1 （Q9LBR1） 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

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 4ISQ	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
4V11 Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84 Deposited 2014-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 273–422（150 aa） Fragment：C2B DOMAIN, UNP RESIDUES 273-422	Not recorded	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
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 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYT1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–21； UniProt 33–53 Author chain E； PDBConstruct 1–21； UniProt 33–53 Author chain F； PDBConstruct 1–21； UniProt 33–53

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4isq
Deposition date deposition_date	2013-01-17
Structure title title	Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I
Keywords keywords	Membrane binding, Synaptotagmin and Ganglioside binding, TOXIN; TOXIN
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	42.45 Å
Radius of gyration Rg (electron density) rg_electron	41.77 Å
Forward intensity I(0) i0	342514000.00
Molecular weight molecular_weight	151900.0 kDa
Excluded volume excluded_volume	189890 Å³
Envelope volume envelope_volume	255420 Å³
Hydration-shell volume shell_volume	51159 Å³
Envelope diameter envelope_diameter	142.4 Å
Shell Rg shell_rg	46.75 Å
Envelope Rg envelope_rg	41.13 Å
Shape Rg shape_rg	41.77 Å
Total Rg total_rg	42.04 Å
Total atoms total_atoms	10682
Residues n_residues	1286
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	133.7 Å
Rg (real space) rg_real	42.37 Å
Rg uncertainty (real space) rg_real_error	1.26 Å
I(0) (real space) i0_real	3.4250e+08
I(0) uncertainty (real space) i0_real_error	5.7890e+06
Rg (reciprocal space) rg_reciprocal	42.45 Å
I(0) (reciprocal space) i0_reciprocal	342500000.0000
Solution quality estimate total_estimate	0.8948
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	61.4 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.731
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	87680000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.820

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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	Neurotoxin
Molecular weight formula_weight	50065.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	10970

MHHHHHHYFSINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS

来源 Source

来源生物 organism	Clostridium botulinum
NCBI Class编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Synaptotagmin-1
Molecular weight formula_weight	2471.8 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

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

GEGKEDAFSKLKEKFMNELHK

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	20

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	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4isqA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4isqA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4isqB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4isqB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4isqC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4isqC02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	164.227 Å
Unit-cell length b length_b	57.550 Å
Unit-cell length c length_c	165.274 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	48.650 Å
R factor r_factor	0.2045
R_work r_work	0.2036
R_free r_free	0.2201

fit	/app/data/saxs_computation/is/4isq/4isq.fit
pddf	/app/data/pr_computation/is/4isq/4isq.pr.out
profile	/app/data/saxs_computation/is/4isq/4isq.dat

Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I

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

Neurotoxin

State in the Current Structure

Other States of the Same Protein in the Database

Synaptotagmin-1

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) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)