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3fie

Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1)

Method: X-RAY DIFFRACTION Dmax: 99.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BOTULINUM NEUROTOXIN TYPE F

Clostridium botulinum

UniProt Q57236

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 1–419 Fragment：residues 1-419, catalytic domain fragment of Vesicle-associated membrane protein 2 × 1 （P63027） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.10 Å R-free 0.279
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–419 Fragment：residues 1-419, catalytic domain fragment of Vesicle-associated membrane protein 2 × 1 （P63027） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.10 Å R-free 0.279

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 3FIE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FII Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh2) Deposited 2008-12-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–419（419 aa） Fragment：residues 1-419, catalytic domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.17 Å R-free 0.290
3FUQ Glycosylated SV2 and Gangliosides as Dual Receptors for Botulinum Neurotoxin Serotype F Deposited 2009-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 862–1278（417 aa） Fragment：sequence database residues 862-1278
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；0.1 M Tris-HCL, 18% ethanol and 150 mM NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.10 Å R-free 0.243
3RSJ Structure of HCRF in complex with Ganglioside GD1a Deposited 2011-05-02 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 866–1278（413 aa） Fragment：Receptor Binding Domain (UNP Residues 866-1276)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K
Resolution 2.00 Å R-free 0.263
3RSJ Structure of HCRF in complex with Ganglioside GD1a Deposited 2011-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 866–1278（413 aa） Fragment：Receptor Binding Domain (UNP Residues 866-1276)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K
Resolution 2.00 Å R-free 0.263
3RSJ Structure of HCRF in complex with Ganglioside GD1a Deposited 2011-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 866–1278（413 aa） Fragment：Receptor Binding Domain (UNP Residues 866-1276)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K
Resolution 2.00 Å R-free 0.263
3RSJ Structure of HCRF in complex with Ganglioside GD1a Deposited 2011-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain D 866–1278（413 aa） Fragment：Receptor Binding Domain (UNP Residues 866-1276)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K
Resolution 2.00 Å R-free 0.263

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

View Construct and Data Evidence
UniProt name Q57236_CLOBO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–419； UniProt 1–419 Author chain B； PDBConstruct 1–419； UniProt 1–419

fragment of Vesicle-associated membrane protein 2

OrganismNot specified

UniProt P63027

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 22–58 Fragment：residues 22-58 Mutation：Q58DCY Non-standard monomer：Yes (specific site not provided by mmCIF) BOTULINUM NEUROTOXIN TYPE F × 1 （Q57236） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.10 Å R-free 0.279
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 22–58 Fragment：residues 22-58 Mutation：Q58DCY Non-standard monomer：Yes (specific site not provided by mmCIF) BOTULINUM NEUROTOXIN TYPE F × 1 （Q57236） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.10 Å R-free 0.279

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 3FIE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FII Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh2) Deposited 2008-12-11 Different construct Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–53（32 aa） Fragment：residues 27-58
Mutation：Q58DCY Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.17 Å R-free 0.290
3RK2 Truncated SNARE complex Deposited 2011-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.268
3RK2 Truncated SNARE complex Deposited 2011-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.268
3RK3 Truncated SNARE complex with complexin Deposited 2011-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.50 Å R-free 0.316
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain Q 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain U 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain Y 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain c 28–60（33 aa） Fragment：UNP residues 28-60
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K
Resolution 3.80 Å R-free 0.345
7UDC cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 Deposited 2022-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 29–83（55 aa）
Mutation：Q36C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9CKX Crystal structure of Dsk2 Sti1 domain bound to a transmembrane domain Deposited 2024-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 95–114（20 aa）
Chain B 95–114（20 aa）
Mutation：I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment Mutation：I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5% MPD, 100 mM Tris pH 8.5
Resolution 1.98 Å R-free 0.232

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VAMP2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–37； UniProt 22–58 Author chain D； PDBConstruct 1–37； UniProt 22–58

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 3fie

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fie
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fie
Deposition date deposition_date2008-12-11
Structure title titleCrystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1)
Keywords keywords;Clostridium botulinum, BoNT F, VAMP, inhibitor, complex structure, Acetylation, Cell junction, HYDROLASE, TOXIN-PROTEIN TRANSPORT COMPLEX ;; HYDROLASE, TOXIN/PROTEIN TRANSPORT
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_guinier31.61 Å
Radius of gyration Rg (electron density) rg_electron30.74 Å
Forward intensity I(0) i0150909000.00
Molecular weight molecular_weight99742.0 kDa
Excluded volume excluded_volume125440 ų
Envelope volume envelope_volume151820 ų
Hydration-shell volume shell_volume40782 ų
Envelope diameter envelope_diameter101.4 Å
Shell Rg shell_rg38.24 Å
Envelope Rg envelope_rg30.58 Å
Shape Rg shape_rg30.72 Å
Total Rg total_rg31.43 Å
Total atoms total_atoms7041
Residues n_residues875
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 dmax99.5 Å
Rg (real space) rg_real31.58 Å
Rg uncertainty (real space) rg_real_error0.76 Å
I(0) (real space) i0_real1.5090e+08
I(0) uncertainty (real space) i0_real_error2.3160e+06
Rg (reciprocal space) rg_reciprocal31.60 Å
I(0) (reciprocal space) i0_reciprocal150900000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.8 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.552
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44030000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.934
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3fiea_
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
Domain ID domain_idd3fieb_
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 (2 domains)

Domain ID domain_id3fieA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1240 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain like
Domain ID domain_id3fieB00
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)