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- PDB-6thy: Botulinum neurotoxin A3 Hc domain in complex with GD1a -

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Basic information

Entry
Database: PDB / ID: 6thy
TitleBotulinum neurotoxin A3 Hc domain in complex with GD1a
ComponentsBoNT/A3
KeywordsTOXIN / Botulinum / neurotoxin / ganglioside / GD1a
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / : / 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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / BoNT/A3
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M.
CitationJournal: Febs Open Bio / Year: 2020
Title: Crystal structure of botulinum neurotoxin subtype A3 cell binding domain in complex with GD1a co-receptor ganglioside.
Authors: Gregory, K.S. / Liu, S.M. / Acharya, K.R.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / 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_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: BoNT/A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1418
Polymers50,4641
Non-polymers1,6777
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint21 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.228, 73.129, 140.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein BoNT/A3 / Neurotoxin type A


Mass: 50464.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3LRX9
#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

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Non-polymers , 5 types, 365 molecules

#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.45 % / Description: Cluster
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Sodium acetate, 22% v/v PEG Smear broad (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4. ...Details: 0.1 M Sodium acetate, 22% v/v PEG Smear broad (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.75→140.18 Å / Num. obs: 47739 / % possible obs: 99.8 % / Redundancy: 26.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 22.5 % / Rmerge(I) obs: 2.99 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2570 / CC1/2: 0.75 / Rpim(I) all: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f0o

6f0o


Resolution: 1.75→70.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.166 / Average fsc free: 0.9204 / Average fsc work: 0.9283 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2129 1904 3.995 %
Rwork0.1784 45755 -
all0.18 --
obs-47659 99.703 %
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: 24.222 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å20 Å2
2--1.447 Å2-0 Å2
3----0.677 Å2
Refinement stepCycle: LAST / Resolution: 1.75→70.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 113 359 3829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133648
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173341
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.6624924
X-RAY DIFFRACTIONr_angle_other_deg2.4961.6077784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8585425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52923.485198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59215647
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg50.641151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2021518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023977
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02758
X-RAY DIFFRACTIONr_nbd_refined0.1930.2540
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.23108
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21671
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.211
X-RAY DIFFRACTIONr_nbd_other0.2370.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.216
X-RAY DIFFRACTIONr_mcbond_it2.1312.271689
X-RAY DIFFRACTIONr_mcbond_other2.1272.2681687
X-RAY DIFFRACTIONr_mcangle_it3.23.3832117
X-RAY DIFFRACTIONr_mcangle_other3.23.3862118
X-RAY DIFFRACTIONr_scbond_it3.222.7191959
X-RAY DIFFRACTIONr_scbond_other3.222.7211960
X-RAY DIFFRACTIONr_scangle_it4.9233.9122807
X-RAY DIFFRACTIONr_scangle_other4.9223.9142808
X-RAY DIFFRACTIONr_lrange_it6.39527.1173995
X-RAY DIFFRACTIONr_lrange_other6.39527.1293996
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.2641300.27233430.27134820.840.82899.74150.255
1.795-1.8450.2781400.23631950.23833690.8680.87698.99080.218
1.845-1.8980.271220.2231640.22233190.8890.90499.00570.198
1.898-1.9560.2671180.20331000.20532220.8910.91799.87590.179
1.956-2.0210.2341110.19329440.19530750.9120.9299.34960.173
2.021-2.0910.2061250.20228940.20230350.9060.91499.47280.177
2.091-2.170.2021150.16728020.16829280.9490.95299.62430.148
2.17-2.2590.221060.1827090.18128180.930.93799.89350.159
2.259-2.3590.2111020.16625900.16826950.9380.95199.88870.148
2.359-2.4740.2351030.17624670.17925740.9340.94299.84460.159
2.474-2.6080.226940.16623790.16924770.9380.94799.83850.151
2.608-2.7660.222990.17622240.17823230.9370.951000.162
2.766-2.9560.21850.1721230.17122080.9470.9561000.158
2.956-3.1930.2191000.1719740.17220740.9460.9611000.161
3.193-3.4970.202880.18718300.18819180.9530.9541000.179
3.497-3.9080.192800.16316450.16417250.9640.9671000.159
3.908-4.5110.17670.1414860.14215530.9680.9771000.14
4.511-5.5190.14440.14712730.14713170.980.9791000.149
5.519-7.780.287490.21210060.21410550.9080.9551000.208
7.78-70.090.216260.2026070.2036340.9560.9599.84230.222

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