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- PDB-3fie: Crystal structure of Clostridium botulinum neurotoxin serotype F ... -

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Basic information

Entry
Database: PDB / ID: 3fie
TitleCrystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1)
Components
  • BOTULINUM NEUROTOXIN TYPE F
  • fragment of Vesicle-associated membrane protein 2
KeywordsHYDROLASE / TOXIN/PROTEIN TRANSPORT / Clostridium botulinum / BoNT F / VAMP / inhibitor / complex structure / Acetylation / Cell junction / TOXIN-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


Toxicity of tetanus toxin (tetX) / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type G (botG) / Toxicity of botulinum toxin type D (botD) / regulation of delayed rectifier potassium channel activity / trans-Golgi Network Vesicle Budding / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex ...Toxicity of tetanus toxin (tetX) / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type G (botG) / Toxicity of botulinum toxin type D (botD) / regulation of delayed rectifier potassium channel activity / trans-Golgi Network Vesicle Budding / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / clathrin-sculpted monoamine transport vesicle membrane / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / zymogen granule membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / eosinophil degranulation / Norepinephrine Neurotransmitter Release Cycle / vesicle fusion / SNARE complex / Golgi to plasma membrane protein transport / SNAP receptor activity / regulation of vesicle-mediated transport / Glutamate Neurotransmitter Release Cycle / bontoxilysin / calcium-ion regulated exocytosis / positive regulation of intracellular protein transport / host cell presynaptic membrane / regulation of exocytosis / host cell cytoplasmic vesicle / neuron projection terminus / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / syntaxin binding / host cell cytosol / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Other interleukin signaling / Golgi Associated Vesicle Biogenesis / Insulin processing / exocytosis / synaptic vesicle exocytosis / synaptic vesicle endocytosis / protein transmembrane transporter activity / response to glucose / vesicle-mediated transport / SNARE binding / secretory granule membrane / secretory granule / long-term synaptic potentiation / Regulation of insulin secretion / Translocation of SLC2A4 (GLUT4) to the plasma membrane / phospholipid binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / synaptic vesicle membrane / metalloendopeptidase activity / cellular response to insulin stimulus / calcium-dependent protein binding / synaptic vesicle / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / toxin activity / cytoplasmic vesicle / protein-containing complex assembly / vesicle / membrane fusion / calmodulin binding / neuron projection / intracellular membrane-bounded organelle / synapse / lipid binding / host cell plasma membrane / perinuclear region of cytoplasm / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain ...Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type F / Vesicle-associated membrane protein 2 / Neurotoxin type F
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAgarwal, R. / Swaminathan, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Mode of VAMP substrate recognition and inhibition of Clostridium botulinum neurotoxin F.
Authors: Agarwal, R. / Schmidt, J.J. / Stafford, R.G. / Swaminathan, S.
History
DepositionDec 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOTULINUM NEUROTOXIN TYPE F
B: BOTULINUM NEUROTOXIN TYPE F
C: fragment of Vesicle-associated membrane protein 2
D: fragment of Vesicle-associated membrane protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1846
Polymers106,0534
Non-polymers1312
Water6,287349
1
A: BOTULINUM NEUROTOXIN TYPE F
C: fragment of Vesicle-associated membrane protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0923
Polymers53,0262
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-53 kcal/mol
Surface area18310 Å2
MethodPISA
2
B: BOTULINUM NEUROTOXIN TYPE F
D: fragment of Vesicle-associated membrane protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0923
Polymers53,0262
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-56 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.637, 61.389, 70.027
Angle α, β, γ (deg.)94.24, 89.92, 113.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein BOTULINUM NEUROTOXIN TYPE F / E.C.3.4.24.69 / BoNT/F (Neurotoxin type F)


Mass: 48745.621 Da / Num. of mol.: 2 / Fragment: residues 1-419, catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bonT/F / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q57236, UniProt: A7GBG3*PLUS, bontoxilysin
#2: Protein/peptide fragment of Vesicle-associated membrane protein 2 / VAMP-2 / Synaptobrevin-2


Mass: 4280.842 Da / Num. of mol.: 2 / Fragment: residues 22-58 / Mutation: Q58DCY / Source method: obtained synthetically / Details: Sequence occurs in Homo sapiens / References: UniProt: P63027
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2008 / Details: mirrors
RadiationMonochromator: si(iii) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→40.65 Å / Num. all: 48376 / Num. obs: 48376 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.19 / Num. unique all: 4368 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
Cootmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A8A

2a8a


Resolution: 2.1→40.65 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 123485.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1420 3 %RANDOM
Rwork0.228 ---
all0.2281 48376 --
obs0.2281 47160 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6656 Å2 / ksol: 0.35665 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å23.16 Å2-0.55 Å2
2--3.31 Å21.51 Å2
3----1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7039 0 2 349 7390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 227 3 %
Rwork0.271 7226 -
obs-48376 90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramdcys.top-org
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4dcys.param-org

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