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- PDB-3dda: Crystal structure of the catalytic domain of Botulinum neurotoxin... -

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Basic information

Entry
Database: PDB / ID: 3dda
TitleCrystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a snap-25 peptide
Components
  • Botulinum neurotoxin A light chain
  • Synaptosomal-associated protein 25
KeywordsHYDROLASE / BOTULINUM NEUROTOXIN TYPE A / BOTOX / CATALYTIC DOMAIN / ENDOPEPTIDASE / SYNTAXIN / BIO-WARFARE AGENT / METAL-BINDING / METALLOPROTEASE / PROTEASE / SECRETED / TRANSMEMBRANE / ZINC / ENZYME-SUBSTRATE COMPLEX / Pharmaceutical / Alternative splicing / Cell junction / Coiled coil / Lipoprotein / Palmitate / Phosphoprotein / Synapse / Synaptosome
Function / homology
Function and homology information


Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / synaptic vesicle fusion to presynaptic active zone membrane / host cell junction / 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 C (botC) / neurotransmitter uptake / synaptic vesicle fusion to presynaptic active zone membrane / host cell junction / 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 / negative regulation of neurotransmitter secretion / 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 / Sensory processing of sound by inner hair cells of the cochlea / Other interleukin signaling / 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 / membrane => GO:0016020 / 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 / 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 ...Synaptosomal-associated protein 25 / 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 / 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 A / Botulinum neurotoxin type A / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsKumaran, D. / Swaminathan, S.
CitationJournal: Plos Pathog. / Year: 2008
Title: Substrate binding mode and its implication on drug design for botulinum neurotoxin A
Authors: Kumaran, D. / Rawat, R. / Ahmed, S.A. / Swaminathan, S.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn_type / 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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Source and taxonomy / Structure summary
Category: pdbx_entity_src_syn / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin A light chain
B: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3114
Polymers50,1502
Non-polymers1612
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-48.5 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.143, 66.192, 64.818
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Botulinum neurotoxin A light chain / Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 49415.727 Da / Num. of mol.: 1 / Fragment: residues 1-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: Hall / Gene: botA / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-RIL
References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Protein/peptide Synaptosomal-associated protein 25 / SNAP-25 / Synaptosomal-associated 25 kDa protein / Super protein / SUP


Mass: 733.903 Da / Num. of mol.: 1 / Fragment: sequence database residues 197-202 / Source method: obtained synthetically
Details: The SNAP-25 peptide is naturally found in Homo sapiens.
Source: (synth.) synthetic construct (others) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG8000, 0.2M Ammoium Sulfate, 0.1M Sodium Cacodylate, 5% Ethylene Glycol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2008 / Details: mirrors
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 64562 / Num. obs: 64562 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2 / Num. unique all: 4397 / % possible all: 80

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3BWI

3bwi


Resolution: 1.5→39.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 66746.27 / 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
Rfree0.2 3193 5.1 %RANDOM
Rwork0.183 ---
obs0.183 62883 95.7 %-
all-62883 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4944 Å2 / ksol: 0.366446 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å20 Å20.31 Å2
2---1.48 Å20 Å2
3----1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 7 375 3854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 468 5.3 %
Rwork0.211 8387 -
obs--81.6 %

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