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6es1

Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C

Method: X-RAY DIFFRACTION Dmax: 84.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Botulinum neurotoxin type A

Clostridium botulinum

UniProt Q45894

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 874–1296 Fragment：Binding domain, UNP residues 874-1296 Synaptic vesicle glycoprotein 2C × 1 （Q496J9） ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000 Resolution 2.00 Å R-free 0.230

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 6ES1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E1H Crystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain, self-inhibiting Zn endopeptidase. Deposited 2000-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–250（241 aa） Fragment：RESIDUES 10-250
Chain B 251–416（166 aa） Fragment：RESIDUES 252-416
Chain C 10–250（241 aa） Fragment：RESIDUES 10-250
Chain D 251–416（166 aa） Fragment：RESIDUES 252-416
Mutation：YES Mutation：YES ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；HANGING DROP VAPOUR DIFFUSION, DROP: 4UL 5MG/ML PROTEIN & 2UL WELL. PROTEIN: 0.05M TRIS PH 8.0,10% GLYCEROL, 0.1% TRITON X-100,1.0MM 2-ME,4% XYLITOL. WELL: 0.2M (NH4)2SO4,0.1M NAOAC PH 4.6, 25% PEG4000.
Resolution 1.80 Å R-free 0.237
2G7K Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；0.1M HEPES buffer, 30% PEG1500, 0.1M NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.80 Å R-free 0.265
2G7K Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28 Different construct 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；0.1M HEPES buffer, 30% PEG1500, 0.1M NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.80 Å R-free 0.265
2G7N Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Not recorded ZN ZINC ION × 1 AG SILVER ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Sodium cacodylate, 28% PEG4K, 0.2M ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.90 Å R-free 0.248
2G7P Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Mutation：R362A, Y365F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, 24% PEG4K, 0.2M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.30 Å R-free 0.275
2G7P Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Mutation：R362A, Y365F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, 24% PEG4K, 0.2M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.30 Å R-free 0.275
2G7Q Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Mutation：R362A, Y365F ZN ZINC ION × 1 AHL N-HYDROXY-L-ARGININAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, PEG4K, 0.2 M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.41 Å R-free 0.261
2G7Q Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28 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 2–425（424 aa） Fragment：Light Chain A, residues 2-425
Mutation：R362A, Y365F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, PEG4K, 0.2 M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.41 Å R-free 0.261
5MOY Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C Deposited 2016-12-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 871–1296（426 aa） Fragment：UNP residues 871-1296
Not recorded EDO 1,2-ETHANEDIOL × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；285 K；20% PEG 8000, 65 mM Hepes
Resolution 2.30 Å R-free 0.251

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BXA2_CLOBO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 23–445； UniProt 874–1296

Synaptic vesicle glycoprotein 2C

Homo sapiens

UniProt Q496J9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 474–567 Fragment：luminal domain 4, UNP residues 474-567 Botulinum neurotoxin type A × 1 （Q45894） ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000 Resolution 2.00 Å R-free 0.230

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 6ES1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4JRA CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C Deposited 2013-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 456–574（119 aa）
Not recorded CL CHLORIDE ION × 6 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；100 mM Hepes pH 7.5, 6% PEG 8000, 8% Glycerol, 100 mM NaCl, VAPOR DIFFUSION, temperature 293K
Resolution 2.30 Å R-free 0.269
4JRA CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C Deposited 2013-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 456–574（119 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；100 mM Hepes pH 7.5, 6% PEG 8000, 8% Glycerol, 100 mM NaCl, VAPOR DIFFUSION, temperature 293K
Resolution 2.30 Å R-free 0.269
5JLV Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C Deposited 2016-04-27 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 C 473–567（95 aa） Fragment：UNP residues 473-567
Not recorded ACT ACETATE ION × 1 PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium acetate pH 4.6, 20% PEG 3350, 0.2 M ammonium phosphate monobasic, 4% polypropylene glycol P 400
Resolution 2.00 Å R-free 0.216
5JLV Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C Deposited 2016-04-27 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 D 473–567（95 aa） Fragment：UNP residues 473-567
Not recorded ACT ACETATE ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium acetate pH 4.6, 20% PEG 3350, 0.2 M ammonium phosphate monobasic, 4% polypropylene glycol P 400
Resolution 2.00 Å R-free 0.216
5MOY Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C Deposited 2016-12-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 456–574（119 aa） Fragment：UNP residues 456-574
Not recorded EDO 1,2-ETHANEDIOL × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；285 K；20% PEG 8000, 65 mM Hepes
Resolution 2.30 Å R-free 0.251

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SV2C_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 24–117； UniProt 474–567

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 6es1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6es1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6es1
Deposition date deposition_date2017-10-19
Structure title titleCrystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C
Keywords keywordsReceptor, Human, Clostridium botulinum, Binding domain, SV2C, PROTEIN BINDING; PROTEIN BINDING
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_guinier27.64 Å
Radius of gyration Rg (electron density) rg_electron26.54 Å
Forward intensity I(0) i057401000.00
Molecular weight molecular_weight60073.0 kDa
Excluded volume excluded_volume75550 ų
Envelope volume envelope_volume91056 ų
Hydration-shell volume shell_volume29115 ų
Envelope diameter envelope_diameter87.8 Å
Shell Rg shell_rg33.45 Å
Envelope Rg envelope_rg26.61 Å
Shape Rg shape_rg26.50 Å
Total Rg total_rg27.42 Å
Total atoms total_atoms4238
Residues n_residues515
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 dmax84.9 Å
Rg (real space) rg_real27.58 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real5.7400e+07
I(0) uncertainty (real space) i0_real_error7.8740e+05
Rg (reciprocal space) rg_reciprocal27.60 Å
I(0) (reciprocal space) i0_reciprocal57400000.0000
Solution quality estimate total_estimate0.9106
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.205
Kurtosis Kurtosis kurtosis-0.684
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11120000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6es1a1
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.6 — Clostridium neurotoxins, the second last domain
Domain ID domain_idd6es1a2
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.4 — STI-like
Family Family familyb.42.4.2 — Clostridium neurotoxins, C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id6es1A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id6es1A02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id6es1B00
Class class2 — Mainly Beta
Architecture architecture160 — 3 Solenoid
Topology topology20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily80 — E3 ubiquitin-protein ligase SopA
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8. Citations (1)

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9. Files and Curves (10)