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- PDB-1xtg: Crystal structure of NEUROTOXIN BONT/A complexed with Synaptosoma... -

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Basic information

Entry
Database: PDB / ID: 1xtg
TitleCrystal structure of NEUROTOXIN BONT/A complexed with Synaptosomal-associated protein 25
Components
  • NEUROTOXIN BONT/A
  • Synaptosomal-associated protein 25
KeywordsTOXIN / botox / botulism / exosites
Function / homology
Function and homology information


Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type E (botE) / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / extrinsic component of presynaptic membrane / Toxicity of botulinum toxin type A (botA) ...Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type E (botE) / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / extrinsic component of presynaptic membrane / Toxicity of botulinum toxin type A (botA) / synaptic vesicle docking / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / ribbon synapse / Serotonin Neurotransmitter Release Cycle / SNAP receptor activity / SNARE complex / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / syntaxin-1 binding / Other interleukin signaling / Sensory processing of sound by inner hair cells of the cochlea / endosomal transport / SNARE complex assembly / host cell cytosol / synaptic vesicle priming / regulation of synapse assembly / myosin binding / regulation of neuron projection development / exocytosis / associative learning / synaptic vesicle exocytosis / tertiary granule membrane / voltage-gated potassium channel activity / protein transmembrane transporter activity / long-term memory / axonal growth cone / specific granule membrane / voltage-gated potassium channel complex / photoreceptor inner segment / regulation of insulin secretion / axonogenesis / filopodium / locomotory behavior / Regulation of insulin secretion / trans-Golgi network / positive regulation of insulin secretion / metalloendopeptidase activity / long-term synaptic potentiation / calcium-dependent protein binding / synaptic vesicle / lamellipodium / actin cytoskeleton / presynaptic membrane / growth cone / toxin activity / cell cortex / chemical synaptic transmission / transmembrane transporter binding / cytoskeleton / neuron projection / endosome / protein domain specific binding / neuronal cell body / lipid binding / Neutrophil degranulation / perinuclear region of cytoplasm / host cell plasma membrane / glutamatergic synapse / proteolysis / extracellular region / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Synaptosomal-associated protein 25 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Clostridium neurotoxin, translocation ...Synaptosomal-associated protein 25 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Botulinum neurotoxin type A / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, Molecular replacement / Resolution: 2.1 Å
AuthorsBreidenbach, M.A. / Brunger, A.T.
CitationJournal: Nature / Year: 2004
Title: Substrate recognition strategy for botulinum neurotoxin serotype A
Authors: Breidenbach, M.A. / Brunger, A.T.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROTOXIN BONT/A
B: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3964
Polymers55,2952
Non-polymers1012
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-79 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.000, 86.000, 165.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NEUROTOXIN BONT/A


Mass: 48555.895 Da / Num. of mol.: 1 / Fragment: Light chain / Mutation: E224Q, Y366F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Plasmid: pBN3 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: GenBank: 33321098, UniProt: P0DPI1*PLUS
#2: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP


Mass: 6739.570 Da / Num. of mol.: 1 / Fragment: n2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP25, SNAP / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 De3 / References: UniProt: P60880
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 8000, 200 mM magnesium acetate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 8.2.11
SYNCHROTRONSSRL BL9-22
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 11, 2004
ADSC QUANTUM 3152CCDApr 23, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL SiSINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL SiSINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→76.33 Å / Num. all: 69211 / Num. obs: 68422 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.15 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: SAD, Molecular replacement / Resolution: 2.1→29.92 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 3419 RANDOM
Rwork0.218 --
all0.218 69211 -
obs0.218 68422 -
Refinement stepCycle: LAST / Resolution: 2.1→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 2 372 4271

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