6g5k

Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1

Method: X-RAY DIFFRACTION D_max: 137.4 Å Quality: REASONABLE

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

Botulinum neurotoxin type B

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 857–1291	Not recorded	Synaptotagmin-1 × 1 （P21579）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 857–1291	Not recorded	Synaptotagmin-1 × 1 （P21579）	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

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 6G5K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EPW CRYSTAL STRUCTURE OF CLOSTRIDIUM NEUROTOXIN TYPE B Deposited 2000-03-29	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.233
1F31 CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE Deposited 2000-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.60 Å R-free 0.270
1F82 BOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN Deposited 2000-06-28	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 1–424（424 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；Hepes, Polyethylene glycol MW 4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.276
1G9A CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 3) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.10 Å R-free 0.248
1G9B CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 1) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.00 Å R-free 0.243
1G9C CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 4) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000. MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.35 Å R-free 0.247
1G9D CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 2) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000. MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.20 Å R-free 0.283
1I1E CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH DOXORUBICIN Deposited 2001-02-01	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 1–1290（1290 aa）	Not recorded	DM2 DOXORUBICIN × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.50 Å R-free 0.276
1S0B Crystal structure of botulinum neurotoxin type B at pH 4.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；298 K；PEG 4000, MES, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.235
1S0C Crystal structure of botulinum neurotoxin type B at pH 5.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；PEG 4000, MES, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.240
1S0D Crystal structure of botulinum neurotoxin type B at pH 5.5 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；PEG 4000, MES, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.273
1S0E Crystal structure of botulinum neurotoxin type B at pH 6.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；298 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 6.00	Resolution 1.90 Å R-free 0.232
1S0F Crystal structure of botulinum neurotoxin type B at pH 7.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；PEG 4000, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00	Resolution 2.30 Å R-free 0.288
1S0G Crystal structure of botulinum neurotoxin type B apo form Deposited 2003-12-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1290（1290 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.265
1Z0H N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B Deposited 2005-03-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 853–1290（438 aa） Fragment：sequence database residues 853-1290	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Ammonium Formate, PEG6000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.282
1Z0H N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B Deposited 2005-03-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 853–1290（438 aa） Fragment：sequence database residues 853-1290	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Ammonium Formate, PEG6000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.282
2ETF Crystal structure of full length botulinum neurotoxin (Type B) light chain Deposited 2005-10-27	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 0–440（441 aa） Fragment：Catalytic Domain (residues 0-440)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；Ammonium sulphate, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP	Resolution 2.29 Å R-free 0.264
2ETF Crystal structure of full length botulinum neurotoxin (Type B) light chain Deposited 2005-10-27	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 0–440（441 aa） Fragment：Catalytic Domain (residues 0-440)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；Ammonium sulphate, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP	Resolution 2.29 Å R-free 0.264
2NM1 Structure of BoNT/B in complex with its protein receptor Deposited 2006-10-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 857–1290（434 aa） Fragment：receptor binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；13% PEG 6000, 0.1M Hepes, pH 7.0, EVAPORATION, temperature 293K	Resolution 2.15 Å R-free 0.246
2NP0 Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain Deposited 2006-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.62 Å R-free 0.227
2NP0 Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain Deposited 2006-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 6 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.62 Å R-free 0.227
2XHL Structure of a functional derivative of Clostridium botulinum neurotoxin type B Deposited 2010-06-18	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 1–437（437 aa） Fragment：RESIDUES 1-437 Chain B 446–858（413 aa） Fragment：RESIDUES 446-858	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；15% PEG3350, 0.1M BIS-TRIS-PROPANE PH 6.5, 0.2M SODIUM SULPHATE	Resolution 2.80 Å R-free 0.282
3ZUQ Crystal structure of an engineered botulinum neurotoxin type B - derivative, LC-B-GS-Hn-B Deposited 2011-07-19	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 1–437（437 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-437, TRANSLOCATION DOMAIN, RESIDUES 446-858 Chain A 446–858（413 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-437, TRANSLOCATION DOMAIN, RESIDUES 446-858	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1M TRIS ACETATE PH8.0, 0.2M MGCL, 20% PEG8000	Resolution 2.70 Å R-free 0.281
4KBB Structure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1a Deposited 2013-04-23	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 A 857–1291（435 aa） Fragment：UNP residues 857-1291	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；292 K；0.2 M MgCl2, 0.1 M Hepes pH 7.0 -7.2 and 20-24% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.189
4KBB Structure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1a Deposited 2013-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 857–1291（435 aa） Fragment：UNP residues 857-1291	Not recorded	CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；292 K；0.2 M MgCl2, 0.1 M Hepes pH 7.0 -7.2 and 20-24% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.189
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VMR Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4 Deposited 2017-04-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 5.0, 10 % PEG8000	Resolution 1.95 Å R-free 0.206
5VMR Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4 Deposited 2017-04-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 5.0, 10 % PEG8000	Resolution 1.95 Å R-free 0.206
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1291（1291 aa） Chain B 1–1291（1291 aa）	Mutation：E231Q, H234Y Mutation：E231Q, H234Y	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
6G5G Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 2 Deposited 2018-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1291（1291 aa） Chain B 1–1291（1291 aa）	Mutation：E231Q, H234Y Mutation：E231Q, H234Y	MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ACT ACETATE ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；0.2 M magnesium chloride, Tris pH 7.0, 10% w/v PEG 8000	Resolution 2.00 Å R-free 0.223
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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 857–1291（435 aa）	Mutation：I1248W, V1249W	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
6UC6 Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11 Deposited 2019-09-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M KCl, 15 % PEG 5000 MME, 0.1 M MES	Resolution 2.32 Å R-free 0.222
6UC6 Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11 Deposited 2019-09-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M KCl, 15 % PEG 5000 MME, 0.1 M MES	Resolution 2.32 Å R-free 0.222
6UFT Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLK-G12 Deposited 2019-09-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M ammonium sulfate, 14 % PEG 8000, 0.1 M MES pH 6.0	Resolution 2.90 Å R-free 0.258
6UHT Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10 Deposited 2019-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；15 % PEG 20000 and 0.1 M MES pH 6.5	Resolution 2.20 Å R-free 0.211
6UHT Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10 Deposited 2019-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；15 % PEG 20000 and 0.1 M MES pH 6.5	Resolution 2.20 Å R-free 0.211
6UL4 Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLO-G11 Deposited 2019-10-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa） Fragment：receptor-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20 % Ethanol, 0.1 M Tris	Resolution 3.18 Å R-free 0.258
7NA9 Crystal structure of BoNT/B-LC-JSG-C1 Deposited 2021-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–441（441 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG4000	Resolution 1.76 Å R-free 0.205
7QFQ Cryo-EM structure of Botulinum neurotoxin serotype B Deposited 2021-12-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1291（1291 aa）	Mutation：E231Q, H234Y	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH7.5, 50mM NaCl, 0.5mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7T5F Botulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10 Deposited 2021-12-12	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 A 1–425（425 aa）	Not recorded	ZN ZINC ION × 1 IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M KI, 0.1 M MES pH 6.5, 25 % PEG 4000	Resolution 2.60 Å R-free 0.222
7T5F Botulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10 Deposited 2021-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–425（425 aa）	Not recorded	ZN ZINC ION × 1 IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M KI, 0.1 M MES pH 6.5, 25 % PEG 4000	Resolution 2.60 Å R-free 0.222

33 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BXB_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–459； UniProt 857–1291 Author chain B； PDBConstruct 25–459； UniProt 857–1291

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 C； UniProt 33–53	Not recorded	Botulinum neurotoxin type B × 1 （P10844）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain 33； UniProt 33–53	Not recorded	Botulinum neurotoxin type B × 1 （P10844）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6G5K	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 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 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 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 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
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 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
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 oligomeric state 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 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 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 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 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 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 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 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 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 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 30 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 33； PDBConstruct 1–21； UniProt 33–53 Author chain C； 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.

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	6g5k
Deposition date deposition_date	2018-03-29
Structure title title	Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1
Keywords keywords	botulinum toxin, neurotoxin, protein engineering, receptor 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	38.66 Å
Radius of gyration Rg (electron density) rg_electron	39.13 Å
Forward intensity I(0) i0	156831000.00
Molecular weight molecular_weight	105260.0 kDa
Excluded volume excluded_volume	133130 Å³
Envelope volume envelope_volume	172280 Å³
Hydration-shell volume shell_volume	39342 Å³
Envelope diameter envelope_diameter	143.8 Å
Shell Rg shell_rg	41.30 Å
Envelope Rg envelope_rg	39.05 Å
Shape Rg shape_rg	39.13 Å
Total Rg total_rg	39.27 Å
Total atoms total_atoms	7455
Residues n_residues	876
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	137.4 Å
Rg (real space) rg_real	39.19 Å
Rg uncertainty (real space) rg_real_error	1.55 Å
I(0) (real space) i0_real	1.5680e+08
I(0) uncertainty (real space) i0_real_error	2.9820e+06
Rg (reciprocal space) rg_reciprocal	38.87 Å
I(0) (reciprocal space) i0_reciprocal	156800000.0000
Solution quality estimate total_estimate	0.5948
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.587
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48990000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.667; Smooth: 0.620

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Botulinum neurotoxin type B
Molecular weight formula_weight	55157.1 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7923

MGSSHHHHHHSSGLVPRGSHMASMNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTELQ

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 BL21(DE3)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,33

GEGKEDAFSKLKEKFMNELHK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	439

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8. Citations (1)

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Unit-cell length a length_a	48.300 Å
Unit-cell length b length_b	212.790 Å
Unit-cell length c length_c	52.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	53.250 Å
R factor r_factor	0.1957
R_work r_work	0.1936
R_free r_free	0.2354

fit	/app/data/saxs_computation/g5/6g5k/6g5k.fit
pddf	/app/data/pr_computation/g5/6g5k/6g5k.pr.out
profile	/app/data/saxs_computation/g5/6g5k/6g5k.dat

Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1

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

Botulinum neurotoxin type B

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)