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- PDB-5moy: Crystal structure of the BoNT/A2 receptor-binding domain in compl... -

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Basic information

Entry
Database: PDB / ID: 5moy
TitleCrystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C
Components
  • Botulinum neurotoxin type A
  • Synaptic vesicle glycoprotein 2C
KeywordsHYDROLASE / BETA-HELIX / VESICLES / LUMEN / TOXIN / BOTOX
Function / homology
Function and homology information


Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type A (botA) / dopaminergic synapse / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / neurotransmitter transport / host cell cytosol / regulation of synaptic vesicle exocytosis ...Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type A (botA) / dopaminergic synapse / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / neurotransmitter transport / host cell cytosol / regulation of synaptic vesicle exocytosis / transmembrane transporter activity / protein transmembrane transporter activity / metalloendopeptidase activity / synaptic vesicle membrane / synaptic vesicle / toxin activity / chemical synaptic transmission / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Synaptic vesicle protein SV2 / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain ...Synaptic vesicle protein SV2 / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / 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 / Major facilitator superfamily / Major Facilitator Superfamily / Pectate Lyase C-like / Kunitz inhibitor STI-like superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / 3 Solenoid / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A2 / Synaptic vesicle glycoprotein 2C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 Å
AuthorsBenoit, R.M. / Scharer, M.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163449 Switzerland
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C.
Authors: Benoit, R.M. / Scharer, M.A. / Wieser, M.M. / Li, X. / Frey, D. / Kammerer, R.A.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Synaptic vesicle glycoprotein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0624
Polymers65,5852
Non-polymers4772
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint8 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.740, 91.570, 147.660
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 A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 49600.316 Da / Num. of mol.: 1 / Fragment: UNP residues 871-1296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Production host: Escherichia coli (E. coli) / References: UniProt: Q45894, bontoxilysin
#2: Protein Synaptic vesicle glycoprotein 2C


Mass: 15984.894 Da / Num. of mol.: 1 / Fragment: UNP residues 456-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SV2C, KIAA1054 / Production host: Escherichia coli (E. coli) / References: UniProt: Q496J9
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 8000, 65 mM Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.3→45.785 Å / Num. obs: 29498 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.539 % / Biso Wilson estimate: 49.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.118 / Χ2: 1.05 / Net I/σ(I): 12.56 / Num. measured all: 192878 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.3-2.366.8151.6361.070.5481100
2.36-2.436.9411.3311.330.631100
2.43-2.56.9171.0311.740.711100
2.5-2.576.8830.9152.020.7711100
2.57-2.666.8050.7392.470.8331100
2.66-2.756.7010.5633.30.8771100
2.75-2.866.60.4264.270.9331100
2.86-2.976.3380.3145.770.9551100
2.97-3.15.9030.237.650.971100
3.1-3.266.2380.17110.390.985199.9
3.26-3.436.7570.11815.040.993199.9
3.43-3.646.8130.0919.970.995199.7
3.64-3.896.6220.06924.850.997199.9
3.89-4.26.4090.05828.180.998199.8
4.2-4.66.2910.04633.560.998199.7
4.6-5.156.0670.04234.750.999199.4
5.15-5.945.5140.04331.210.999199.8
5.94-7.286.040.04332.670.999199.8
7.28-10.296.4440.03341.620.9991100
10.29-45.7855.6440.02445.191199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å49.23 Å
Translation2.2 Å49.23 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XSCALEdata scaling
PHASER2.7.8phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vu9, 4jra

2vu9

4jra


Resolution: 2.302→45.785 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1475 5 %
Rwork0.1947 --
obs0.1975 29489 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→45.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4257 0 13 76 4346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014358
X-RAY DIFFRACTIONf_angle_d1.0175879
X-RAY DIFFRACTIONf_dihedral_angle_d11.8952596
X-RAY DIFFRACTIONf_chiral_restr0.057635
X-RAY DIFFRACTIONf_plane_restr0.005748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.37630.33991310.2822501X-RAY DIFFRACTION100
2.3763-2.46120.36981320.26612496X-RAY DIFFRACTION100
2.4612-2.55970.32291320.2512501X-RAY DIFFRACTION100
2.5597-2.67620.29141320.23072523X-RAY DIFFRACTION100
2.6762-2.81730.27661340.22182529X-RAY DIFFRACTION100
2.8173-2.99380.29891320.22592521X-RAY DIFFRACTION100
2.9938-3.22490.33171340.21662536X-RAY DIFFRACTION100
3.2249-3.54930.24761330.20462529X-RAY DIFFRACTION100
3.5493-4.06260.26441340.18352554X-RAY DIFFRACTION100
4.0626-5.11740.18621370.14792595X-RAY DIFFRACTION100
5.1174-45.7940.20841440.18452729X-RAY DIFFRACTION100

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