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- PDB-7ovw: Binding domain of botulinum neurotoxin E in complex with GD1a -

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Basic information

Entry
Database: PDB / ID: 7ovw
TitleBinding domain of botulinum neurotoxin E in complex with GD1a
ComponentsNeurotoxin type E
KeywordsTOXIN / botulinum neurotoxin / ganglioside / toxin receptor / bacterial toxin / carbohydrate binding
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMasuyer, G. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
CitationJournal: Int J Mol Sci / Year: 2021
Title: Mechanism of Ganglioside Receptor Recognition by Botulinum Neurotoxin Serotype E.
Authors: Masuyer, G. / Davies, J.R. / Stenmark, P.
History
DepositionJun 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 29, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / pdbx_database_proc / pdbx_entity_branch_descriptor
Item: _atom_site.calc_flag / _citation.journal_volume ..._atom_site.calc_flag / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Neurotoxin type E
BBB: Neurotoxin type E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4954
Polymers108,6592
Non-polymers1,8362
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, protein is a monomer in solution (size exclusion chromatography ) carbohydrate is bound (observed by ITC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint25 kcal/mol
Surface area34460 Å2
Unit cell
Length a, b, c (Å)69.372, 84.920, 79.903
Angle α, β, γ (deg.)90.000, 91.565, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neurotoxin type E


Mass: 54329.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinant binding domain of botulinum neurotoxin E with N-terminal His and HA tags
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5H0J8
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-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: 998.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-2-4/a4-b1_b4-c1_c3-d1_d3-e2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a4-b1_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M sodium chloride 0.1 M phosphate/citrate pH 4.2, 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→53.77 Å / Num. obs: 44975 / % possible obs: 95.4 % / Redundancy: 3 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.066 / Rrim(I) all: 0.094 / Χ2: 0.88 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3757 / CC1/2: 0.807 / Rpim(I) all: 0.529 / Rrim(I) all: 0.748 / Χ2: 1.22 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFZ

3ffz


Resolution: 2.2→53.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.218 / SU B: 8.149 / SU ML: 0.199 / Average fsc free: 0.8655 / Average fsc work: 0.8852 / Cross valid method: FREE R-VALUE / ESU R: 0.342 / ESU R Free: 0.25
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2709 2082 4.632 %
Rwork0.2165 42870 -
all0.219 --
obs-44952 95.245 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.213 Å2
Baniso -1Baniso -2Baniso -3
1--2.981 Å20 Å21.159 Å2
2--3.566 Å2-0 Å2
3----0.647 Å2
Refinement stepCycle: LAST / Resolution: 2.2→53.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 124 297 7055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186333
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.6559392
X-RAY DIFFRACTIONr_angle_other_deg1.0771.60414511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60524.272405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.449151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5441528
X-RAY DIFFRACTIONr_chiral_restr0.0390.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021760
X-RAY DIFFRACTIONr_nbd_refined0.1620.21041
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.26129
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23247
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0640.23224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2352
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.210
X-RAY DIFFRACTIONr_nbd_other0.1540.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.25
X-RAY DIFFRACTIONr_mcbond_it1.5694.2373235
X-RAY DIFFRACTIONr_mcbond_other1.5694.2363234
X-RAY DIFFRACTIONr_mcangle_it2.7286.354042
X-RAY DIFFRACTIONr_mcangle_other2.7286.3514043
X-RAY DIFFRACTIONr_scbond_it1.4094.3923679
X-RAY DIFFRACTIONr_scbond_other1.4094.3933680
X-RAY DIFFRACTIONr_scangle_it2.4666.5275350
X-RAY DIFFRACTIONr_scangle_other2.4666.5285351
X-RAY DIFFRACTIONr_lrange_it4.3747.3537469
X-RAY DIFFRACTIONr_lrange_other4.35247.3177427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3061690.2972999X-RAY DIFFRACTION91.218
2.257-2.3190.3131490.2873157X-RAY DIFFRACTION96.9786
2.319-2.3860.3231250.2813071X-RAY DIFFRACTION97.737
2.386-2.4590.3221270.2632983X-RAY DIFFRACTION97.6146
2.459-2.540.3181640.2542884X-RAY DIFFRACTION97.2869
2.54-2.6290.31270.2492707X-RAY DIFFRACTION95.3888
2.629-2.7280.2721470.2262662X-RAY DIFFRACTION97.0629
2.728-2.8390.2971320.2362556X-RAY DIFFRACTION96.1717
2.839-2.9660.2991410.2252447X-RAY DIFFRACTION96.5672
2.966-3.110.3171260.2332316X-RAY DIFFRACTION96.2175
3.11-3.2780.291010.2332226X-RAY DIFFRACTION95.3689
3.278-3.4770.291040.2372110X-RAY DIFFRACTION95.3899
3.477-3.7160.279810.2181972X-RAY DIFFRACTION95.2226
3.716-4.0130.219850.1961842X-RAY DIFFRACTION94.3683
4.013-4.3950.203780.1671658X-RAY DIFFRACTION93.183
4.395-4.9120.183570.1471517X-RAY DIFFRACTION93.2464
4.912-5.6680.227600.1651326X-RAY DIFFRACTION92.5234
5.668-6.9330.258720.2131088X-RAY DIFFRACTION91.2667
6.933-9.7690.326280.205860X-RAY DIFFRACTION89.2462
9.769-53.770.31390.225489X-RAY DIFFRACTION86.911

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