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- PDB-3r4u: Cell entry of botulinum neurotoxin type C is dependent upon inter... -

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Basic information

Entry
Database: PDB / ID: 3r4u
TitleCell entry of botulinum neurotoxin type C is dependent upon interaction with two ganglioside molecules
ComponentsBotulinum neurotoxin type C1
KeywordsHYDROLASE / Botulinum Toxins / gangliosides
Function / homology
Function and homology information


symbiont-mediated suppression of host neurotransmitter secretion / ganglioside binding / Toxicity of botulinum toxin type C (botC) / membrane protein proteolysis / negative regulation of calcium ion-dependent exocytosis / bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region
Similarity search - Function
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 / Kunitz inhibitor STI-like superfamily ...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 / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStrotmeier, J. / Gu, S. / Jutzi, S. / Mahrhold, S. / Zhou, J. / Pich, A. / Bigalke, H. / Rummel, A. / Jin, R. / Binz, T.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: The biological activity of botulinum neurotoxin type C is dependent upon novel types of ganglioside binding sites.
Authors: Strotmeier, J. / Gu, S. / Jutzi, S. / Mahrhold, S. / Zhou, J. / Pich, A. / Eichner, T. / Bigalke, H. / Rummel, A. / Jin, R. / Binz, T.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 C1
B: Botulinum neurotoxin type C1


Theoretical massNumber of molelcules
Total (without water)102,8212
Polymers102,8212
Non-polymers00
Water12,809711
1
A: Botulinum neurotoxin type C1


Theoretical massNumber of molelcules
Total (without water)51,4101
Polymers51,4101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type C1


Theoretical massNumber of molelcules
Total (without water)51,4101
Polymers51,4101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.017, 76.496, 106.943
Angle α, β, γ (deg.)90.00, 116.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Botulinum neurotoxin type C1 / BoNT/C1 / Bontoxilysin-C1 / Botulinum neurotoxin C1 heavy chain


Mass: 51410.348 Da / Num. of mol.: 2 / Fragment: HcC domain, UNP residues 867-1291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18640, bontoxilysin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 10%(v/v)PEG4000, 0.1M sodium citrate(pH4.4), 3% 6-aminohexanoic acid, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 2.2→44.1 Å / Num. obs: 71549 / % possible obs: 98.9 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.1 Å / SU ML: 0.26 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 3617 5.06 %
Rwork0.1712 --
obs0.1732 71549 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.842 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3806 Å20 Å2-2.629 Å2
2--9.1724 Å2-0 Å2
3----4.7918 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 0 711 7641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077082
X-RAY DIFFRACTIONf_angle_d1.0219586
X-RAY DIFFRACTIONf_dihedral_angle_d18.0982526
X-RAY DIFFRACTIONf_chiral_restr0.0731020
X-RAY DIFFRACTIONf_plane_restr0.0041242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1995-2.27820.27183210.21896139X-RAY DIFFRACTION90
2.2782-2.36940.25783610.21316832X-RAY DIFFRACTION100
2.3694-2.47720.27053430.20496829X-RAY DIFFRACTION100
2.4772-2.60780.23573450.19346858X-RAY DIFFRACTION100
2.6078-2.77110.23994080.18866776X-RAY DIFFRACTION100
2.7711-2.98510.2293880.1826815X-RAY DIFFRACTION100
2.9851-3.28540.21473690.17216878X-RAY DIFFRACTION100
3.2854-3.76050.18983450.15636875X-RAY DIFFRACTION100
3.7605-4.7370.16183750.12836904X-RAY DIFFRACTION100
4.737-44.11440.18813620.16567026X-RAY DIFFRACTION100

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