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- PDB-2nm1: Structure of BoNT/B in complex with its protein receptor -

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Basic information

Entry
Database: PDB / ID: 2nm1
TitleStructure of BoNT/B in complex with its protein receptor
Components
  • Botulinum neurotoxin type B
  • Synaptotagmin-2
KeywordsTOXIN / HYDROLASE / neurotransmission / botulism / synaptotagmin
Function / homology
Function and homology information


Toxicity of botulinum toxin type B (botB) / calcium-dependent activation of synaptic vesicle fusion / inositol 1,3,4,5 tetrakisphosphate binding / chromaffin granule membrane / dense core granule / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis ...Toxicity of botulinum toxin type B (botB) / calcium-dependent activation of synaptic vesicle fusion / inositol 1,3,4,5 tetrakisphosphate binding / chromaffin granule membrane / dense core granule / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / bontoxilysin / positive regulation of dendrite extension / host cell presynaptic membrane / calcium-dependent phospholipid binding / host cell cytoplasmic vesicle / syntaxin binding / host cell cytosol / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / synaptic vesicle exocytosis / protein transmembrane transporter activity / vesicle-mediated transport / SNARE binding / terminal bouton / neuromuscular junction / metalloendopeptidase activity / synaptic vesicle membrane / toxin activity / cell differentiation / axon / lipid binding / calcium ion binding / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Synaptotagmin / 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 ...Synaptotagmin / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / C2 domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type B / Synaptotagmin-2
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJin, R. / Rummel, A. / Binz, T. / Brunger, A.T.
Citation
Journal: Nature / Year: 2006
Title: Botulinum neurotoxin B recognizes its protein receptor with high affinity and specificity.
Authors: Jin, R. / Rummel, A. / Binz, T. / Brunger, A.T.
#1: Journal: NAT.STRUCT.BIOL. / Year: 2000
Title: Structural analysis of the catalytic and binding sites of Clostridium botulinum neurotoxin B.
Authors: Swaminathan, S. / Eswaramoorthy, S.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B.
Authors: Jayaraman, S. / Eswaramoorthy, S. / Ahmed, S.A. / Smith, L.A. / Swaminathan, S.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
B: Synaptotagmin-2


Theoretical massNumber of molelcules
Total (without water)54,5252
Polymers54,5252
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-11 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.820, 97.520, 113.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B


Mass: 52403.988 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15pREP4 / References: UniProt: P10844, bontoxilysin
#2: Protein/peptide Synaptotagmin-2 / SytII


Mass: 2121.454 Da / Num. of mol.: 1 / Fragment: luminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15pREP4 / References: UniProt: P29101*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 13% PEG 6000, 0.1M Hepes, pH 7.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 32540 / Num. obs: 32377 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.9
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z0H

1z0h


Resolution: 2.15→39.81 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 88482.92 / 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
Rfree0.246 1550 4.8 %RANDOM
Rwork0.199 ---
obs0.199 32377 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8303 Å2 / ksol: 0.337789 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-16.92 Å20 Å20 Å2
2---6.58 Å20 Å2
3----10.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.15→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 0 129 3941
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it4.221.5
X-RAY DIFFRACTIONc_mcangle_it5.642
X-RAY DIFFRACTIONc_scbond_it6.312
X-RAY DIFFRACTIONc_scangle_it8.192.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 214 4.7 %
Rwork0.263 4296 -
obs--80.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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