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1f82

BOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN

Method: X-RAY DIFFRACTION Dmax: 78.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BOTULINUM NEUROTOXIN TYPE B

Clostridium botulinum

UniProt P10844

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–424 Fragment：CATALYTIC DOMAIN 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

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 1F82 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 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
1G9A CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 3) Deposited 2000-11-22 Different construct 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state 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 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 oligomeric state Different ligand/ion 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 857–1291（435 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 857–1291（435 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 mutation/modification 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）
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 oligomeric state 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 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 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 oligomeric state Different ligand/ion 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 oligomeric state 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） 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 oligomeric state 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1291（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 46 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 1–424； UniProt 1–424

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

SAXS scattering curve SAXS Profile

SAXS profile for 1f82

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1f82
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1f82
Deposition date deposition_date2000-06-28
Structure title titleBOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN
Keywords keywordsZinc dependent protease, Botulinum neurotoxin, TOXIN, HYDROLASE; TOXIN,HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.59 Å
Radius of gyration Rg (electron density) rg_electron22.36 Å
Forward intensity I(0) i038327600.00
Molecular weight molecular_weight49014.0 kDa
Excluded volume excluded_volume61827 ų
Envelope volume envelope_volume72238 ų
Hydration-shell volume shell_volume26543 ų
Envelope diameter envelope_diameter82.8 Å
Shell Rg shell_rg29.72 Å
Envelope Rg envelope_rg22.71 Å
Shape Rg shape_rg22.35 Å
Total Rg total_rg23.28 Å
Total atoms total_atoms3456
Residues n_residues424
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.4 Å
Rg (real space) rg_real23.49 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real3.8330e+07
I(0) uncertainty (real space) i0_real_error5.2880e+05
Rg (reciprocal space) rg_reciprocal23.52 Å
I(0) (reciprocal space) i0_reciprocal38330000.0000
Solution quality estimate total_estimate0.8857
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4 Å
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9280000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1f82a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.7 — Clostridium neurotoxins, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id1f82A00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1240 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain like
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8. Citations (1)

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9. Files and Curves (10)