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- PDB-5tpc: Binding domain of BoNT/A complexed with ganglioside -

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Basic information

Entry
Database: PDB / ID: 5tpc
TitleBinding domain of BoNT/A complexed with ganglioside
ComponentsBotulinum neurotoxin type A
KeywordsHYDROLASE / binding domain / lectin / ganglioside binding
Function / homology
Function and homology information


host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
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 A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBerntsson, R.P.-A. / Svensson, L.M. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Glycans Confer Specificity to the Recognition of Ganglioside Receptors by Botulinum Neurotoxin A.
Authors: Hamark, C. / Berntsson, R.P. / Masuyer, G. / Henriksson, L.M. / Gustafsson, R. / Stenmark, P. / Widmalm, G.
History
DepositionOct 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8263
Polymers49,6801
Non-polymers1,1462
Water5,873326
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint13 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.972, 114.302, 106.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1673-

HOH

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Components

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


Mass: 49680.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][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-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG6000, 0.2 M MgCl2, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92526 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92526 Å / Relative weight: 1
ReflectionResolution: 2→63 Å / Num. obs: 30186 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.078 / Net I/σ(I): 10 / Num. measured all: 105978
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.053.50.5652.6778622280.7420.35699
8.94-40.423.20.03127.711473550.9980.0293.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VU9

2vu9


Resolution: 2→62.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2126 / WRfactor Rwork: 0.1794 / FOM work R set: 0.8023 / SU B: 10.183 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2301 / SU Rfree: 0.1811 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1532 5.1 %RANDOM
Rwork0.2027 ---
obs0.2045 28636 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.01 Å2 / Biso mean: 27.222 Å2 / Biso min: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 2→62.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 77 326 3904
Biso mean--69.57 32.36 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023700
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9575017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19224.921191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00115656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9541520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022799
X-RAY DIFFRACTIONr_mcbond_it0.971.3411724
X-RAY DIFFRACTIONr_mcangle_it1.7422.0052162
X-RAY DIFFRACTIONr_scbond_it1.2311.6321976
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 120 -
Rwork0.271 2101 -
all-2221 -
obs--98.67 %
Refinement TLS params.Method: refined / Origin x: 19.7931 Å / Origin y: 24.1511 Å / Origin z: 5.8404 Å
111213212223313233
T0.0374 Å2-0.0036 Å2-0.0006 Å2-0.149 Å2-0.0092 Å2--0.0037 Å2
L0.212 °20.0081 °2-0.2372 °2-1.0955 °2-0.5788 °2--1.6132 °2
S-0.0112 Å °0.0251 Å °-0.0119 Å °0.0961 Å °0.0316 Å °0.0321 Å °-0.1149 Å °-0.0126 Å °-0.0204 Å °

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