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- PDB-4jra: CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING ... -

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Basic information

Entry
Database: PDB / ID: 4jra
TitleCRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C
Components
  • Botulinum neurotoxin type A
  • Synaptic vesicle glycoprotein 2C
KeywordsHYDROLASE / Beta-helix / Vesicles / lumen / toxin
Function / homology
Function and homology information


host cell junction / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type A (botA) / negative regulation of neurotransmitter secretion / bontoxilysin / dopaminergic synapse / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol ...host cell junction / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type A (botA) / negative regulation of neurotransmitter secretion / bontoxilysin / dopaminergic synapse / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / neurotransmitter transport / regulation of synaptic vesicle exocytosis / protein transmembrane transporter activity / transmembrane transporter activity / membrane => GO:0016020 / metalloendopeptidase activity / synaptic vesicle / synaptic vesicle membrane / toxin activity / chemical synaptic transmission / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Pentapeptide repeat region / E3 ubiquitin-protein ligase SopA / : / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain ...Pentapeptide repeat region / E3 ubiquitin-protein ligase SopA / : / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Pectate Lyase C-like / Kunitz inhibitor STI-like superfamily / Major facilitator superfamily / Major Facilitator Superfamily / 3 Solenoid / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / MFS transporter superfamily / Jelly Rolls - #200 / 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 A / Botulinum neurotoxin type A / Synaptic vesicle glycoprotein 2C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBenoit, R.M. / Frey, D. / Wieser, M.M. / Jaussi, R. / Schertler, G.F.X. / Capitani, G. / Kammerer, R.A.
CitationJournal: Nature / Year: 2014
Title: Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A.
Authors: Benoit, R.M. / Frey, D. / Hilbert, M. / Kevenaar, J.T. / Wieser, M.M. / Stirnimann, C.U. / McMillan, D. / Ceska, T. / Lebon, F. / Jaussi, R. / Steinmetz, M.O. / Schertler, G.F. / Hoogenraad, ...Authors: Benoit, R.M. / Frey, D. / Hilbert, M. / Kevenaar, J.T. / Wieser, M.M. / Stirnimann, C.U. / McMillan, D. / Ceska, T. / Lebon, F. / Jaussi, R. / Steinmetz, M.O. / Schertler, G.F. / Hoogenraad, C.C. / Capitani, G. / Kammerer, R.A.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)135,67812
Polymers135,4194
Non-polymers2598
Water1,47782
1
A: Botulinum neurotoxin type A
D: Synaptic vesicle glycoprotein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,96810
Polymers67,7102
Non-polymers2598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Botulinum neurotoxin type A
C: Synaptic vesicle glycoprotein 2C


Theoretical massNumber of molelcules
Total (without water)67,7102
Polymers67,7102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.440, 105.260, 127.960
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 51724.617 Da / Num. of mol.: 2
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: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Protein Synaptic vesicle glycoprotein 2C


Mass: 15984.894 Da / Num. of mol.: 2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Hepes pH 7.5, 6% PEG 8000, 8% Glycerol, 100 mM NaCl, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2012
RadiationMonochromator: FIXED EXIT DOUBLE, CHANNEL DCM MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 67843 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FUO

3fuo


Resolution: 2.3→19.933 Å / Isotropic thermal model: isotropic / σ(F): 1.36 / Phase error: 27.58 / Stereochemistry target values: TWIN_LSQ_F / Details: twin operator -h, -k, l
RfactorNum. reflection% reflection
Rfree0.2692 2033 3 %
Rwork0.2353 --
obs0.24 67843 99.96 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8304 0 8 82 8394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088499
X-RAY DIFFRACTIONf_angle_d1.07911481
X-RAY DIFFRACTIONf_dihedral_angle_d15.3043132
X-RAY DIFFRACTIONf_chiral_restr0.0661229
X-RAY DIFFRACTIONf_plane_restr0.0041475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35370.30091340.3024329X-RAY DIFFRACTION97
2.3537-2.41240.31791340.29454367X-RAY DIFFRACTION97
2.4124-2.47760.35541350.28784353X-RAY DIFFRACTION97
2.4776-2.55030.28061350.28264380X-RAY DIFFRACTION97
2.5503-2.63250.30081340.27744366X-RAY DIFFRACTION97
2.6325-2.72630.3031350.2644373X-RAY DIFFRACTION97
2.7263-2.83520.26441340.26084394X-RAY DIFFRACTION97
2.8352-2.96380.27111360.24964363X-RAY DIFFRACTION97
2.9638-3.11950.28781380.24114431X-RAY DIFFRACTION97
3.1195-3.31410.25621340.23224328X-RAY DIFFRACTION97
3.3141-3.56860.26141360.22664413X-RAY DIFFRACTION97
3.5686-3.92530.2591360.21984400X-RAY DIFFRACTION97
3.9253-4.48750.23141360.19994369X-RAY DIFFRACTION97
4.4875-5.63230.23251360.20114434X-RAY DIFFRACTION97
5.6323-19.85080.31411390.26424488X-RAY DIFFRACTION97

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