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- PDB-8rvh: Structure of the binding domain of BoNT/A mutant Y1117V/H1253K in... -

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Basic information

Entry
Database: PDB / ID: 8rvh
TitleStructure of the binding domain of BoNT/A mutant Y1117V/H1253K in complex with the GD1a ganglioside receptor
ComponentsBotulinum neurotoxin A heavy chain
KeywordsTOXIN / botulinum neurotoxin / receptor binding / ganglioside
Function / homology
Function and homology information


symbiont-mediated suppression of host exocytosis / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity ...symbiont-mediated suppression of host exocytosis / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
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 / Kunitz inhibitor STI-like superfamily ...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 / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMasuyer, G. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Commun Chem / Year: 2025
Title: Botulinum neurotoxin A mutants with enhanced ganglioside binding show improved potency and altered ganglioside selectivity.
Authors: Masuyer, G. / Rummel, A. / Stenmark, P.
History
DepositionFeb 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin A heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9674
Polymers51,6401
Non-polymers1,3263
Water7,710428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.637, 43.582, 133.211
Angle α, β, γ (deg.)90.00, 95.71, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Botulinum neurotoxin A heavy chain / HC


Mass: 51640.391 Da / Num. of mol.: 1 / Mutation: Y1117V, H1253K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bonT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DPI0
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-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 / Feature type: SUBJECT OF INVESTIGATION
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


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT 9.0 25 % w/v PEG 1500 (PACT D6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→66.27 Å / Num. obs: 39384 / % possible obs: 94.8 % / Redundancy: 3.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.074 / Rrim(I) all: 0.108 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1576 / CC1/2: 0.371 / Rpim(I) all: 0.216 / % possible all: 64.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→69.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.942 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20668 1958 5 %RANDOM
Rwork0.1666 ---
obs0.16854 37426 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.84 Å2
2--0.44 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.8→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 88 428 3952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023624
X-RAY DIFFRACTIONr_bond_other_d0.0030.023409
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9644910
X-RAY DIFFRACTIONr_angle_other_deg0.91437823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4775425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44624.945182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67915640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9921519
X-RAY DIFFRACTIONr_chiral_restr0.0910.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02884
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.682.1121694
X-RAY DIFFRACTIONr_mcbond_other1.6782.1081693
X-RAY DIFFRACTIONr_mcangle_it2.8713.1482118
X-RAY DIFFRACTIONr_mcangle_other2.8713.1522119
X-RAY DIFFRACTIONr_scbond_it1.8552.3491930
X-RAY DIFFRACTIONr_scbond_other1.8542.3491930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1093.4482792
X-RAY DIFFRACTIONr_long_range_B_refined5.90417.6084369
X-RAY DIFFRACTIONr_long_range_B_other5.71317.0954170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 101 -
Rwork0.328 1898 -
obs--65.61 %

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