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- PDB-3r4s: Cell entry of botulinum neurotoxin type C is dependent upon inter... -

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Basic information

Entry
Database: PDB / ID: 3r4s
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
N-acetyl-alpha-neuraminic acid / N-acetyl-beta-neuraminic acid / Botulinum neurotoxin type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.2Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0586
Polymers102,8212
Non-polymers1,2374
Water15,673870
1
A: Botulinum neurotoxin type C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0293
Polymers51,4101
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0293
Polymers51,4101
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.381, 77.047, 108.567
Angle α, β, γ (deg.)90.00, 116.73, 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: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID / N-Acetylneuraminic acid


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 870 / 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: 3.57 Å3/Da / Density % sol: 65.59 %
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: MARMOSAIC 325 mm CCD / Detector: CCD / 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: 2.15→44.3 Å / Num. obs: 78700 / % possible obs: 99.6 %

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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: 2.15→44.286 Å / SU ML: 0.25 / σ(F): 1.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 3951 5.02 %RANDOM
Rwork0.1684 ---
obs0.1703 78700 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.196 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9445 Å20 Å2-0.9023 Å2
2--5.7539 Å2-0 Å2
3----4.8094 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6954 0 84 870 7908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077190
X-RAY DIFFRACTIONf_angle_d1.0139742
X-RAY DIFFRACTIONf_dihedral_angle_d19.8532578
X-RAY DIFFRACTIONf_chiral_restr0.0751046
X-RAY DIFFRACTIONf_plane_restr0.0041256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1503-2.22710.2823840.21687315X-RAY DIFFRACTION99
2.2271-2.31630.25583950.19757445X-RAY DIFFRACTION99
2.3163-2.42170.25174000.1897419X-RAY DIFFRACTION100
2.4217-2.54940.21063570.17837468X-RAY DIFFRACTION100
2.5494-2.70910.22823830.18517458X-RAY DIFFRACTION100
2.7091-2.91820.22854070.18197436X-RAY DIFFRACTION100
2.9182-3.21180.22083990.17057508X-RAY DIFFRACTION100
3.2118-3.67640.19233830.15777539X-RAY DIFFRACTION100
3.6764-4.63110.16014230.13177502X-RAY DIFFRACTION100
4.6311-44.29530.18024200.16057660X-RAY DIFFRACTION100

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