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- PDB-2vu9: CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMA... -

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Entry
Database: PDB / ID: 2vu9
TitleCRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN IN COMPLEX WITH GT1B
ComponentsBOTULINUM NEUROTOXIN A HEAVY CHAIN
KeywordsHYDROLASE / METALLOPROTEASE / NEUROTOXIN / GANGLIOSIDE / METAL-BINDING / TOXIN / PROTEASE / MEMBRANE / RECEPTOR / SECRETED
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 / membrane => GO:0016020 / metalloendopeptidase activity / toxin activity ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / membrane => GO:0016020 / 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 / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-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: 1.6 Å
AuthorsStenmark, P. / Dupuy, J. / Stevens, R.C.
CitationJournal: Plos Pathog. / Year: 2008
Title: Crystal Structure of Botulinum Neurotoxin Type a in Complex with the Cell Surface Co-Receptor Gt1B- Insight Into the Toxin-Neuron Interaction.
Authors: Stenmark, P. / Dupuy, J. / Imamura, A. / Kiso, M. / Stevens, R.C.
History
DepositionMay 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOTULINUM NEUROTOXIN A HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0283
Polymers51,7131
Non-polymers1,3142
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.700, 116.110, 105.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BOTULINUM NEUROTOXIN A HEAVY CHAIN / BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN / BONT/A / BONTOXILYSIN-A / BOTOX


Mass: 51713.398 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN, RESIDUES 876-1296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Strain: A / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#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)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1290.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2-3/a4-b1_b3-c2_b4-d1_d3-e1_e3-f2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGT1B (COMPOSED OF BGC, GAL, SIA, NGA): SIX OUT OF THE SEVEN MONOSACCARIDES IN THE GANGLIOSIDE GT1B.

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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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.5 / Details: 21% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 58845 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NYY

2nyy


Resolution: 1.6→19.67 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.744 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2968 5 %RANDOM
Rwork0.161 ---
obs0.162 55875 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 89 397 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223693
X-RAY DIFFRACTIONr_bond_other_d0.0030.022489
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9745013
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0035997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51925.026191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86915654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0031519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
X-RAY DIFFRACTIONr_nbd_refined0.1990.2601
X-RAY DIFFRACTIONr_nbd_other0.1980.22657
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21793
X-RAY DIFFRACTIONr_nbtor_other0.0970.22069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.081.52775
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29823459
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.30331875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.214.51551
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 207
Rwork0.177 4049
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.194-0.69120.75391.73570.05181.83610.0990.2499-0.2613-0.2343-0.0395-0.29030.04210.2934-0.0595-0.0844-0.0140.03470.10260.02460.130832.63232.148-8.717
20.69580.11920.1861.5144-1.17082.3553-0.00190.09330.060.2219-0.1636-0.2502-0.36550.25550.16550.0306-0.0436-0.02480.03520.02940.050724.33540.334-0.525
30.27680.04190.01391.3124-1.48423.5281-0.01790.06640.06930.25840.08460.0208-0.5297-0.23-0.06660.0750.0320.00320.04620.02630.038414.20840.488-0.468
40.9917-0.12420.34561.7235-1.40993.2292-0.00410.14210.03990.1233-0.0166-0.0886-0.25550.0310.0206-0.0026-0.01310.0030.01070.01950.02419.02139.232-4.052
50.2226-0.2697-0.0840.927-0.12891.1047-0.0163-0.0139-0.0237-0.0630.02570.07360.00940.0012-0.00930.055-0.0087-0.02990.04630.00450.072919.514.52511.457
60.19790.43660.00981.1047-0.43611.4854-0.0417-0.0084-0.08570.11970.00210.0979-0.11030.08060.03960.0733-0.0139-0.02050.07160.00070.057319.68416.87319.235
71.59580.325-0.04881.04820.2671.6901-0.0602-0.0731-0.11730.05750.038-0.00920.23850.11830.02210.06420.03030.0030.0184-0.00320.033923.240.36416.243
80.32030.15160.14073.8087-0.64791.5592-0.01190.10290.0768-0.1956-0.05450.19480.0048-0.04450.06640.02690.0078-0.01570.0608-0.00760.021517.1295.7454.63
91.32570.74970.48992.58350.34081.1755-0.08810.09420.054-0.1703-0.01050.44430.0321-0.15830.09860.01830.0055-0.02570.0473-0.0050.08789.3735.89912.391
100.4931-0.2783-1.03553.9234-4.12298.0576-0.0034-0.26580.0640.4752-0.1971-0.2582-0.52720.60250.20050.0796-0.0453-0.06870.0710.01490.012423.59725.81622.45
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A873 - 910
2X-RAY DIFFRACTION2A911 - 966
3X-RAY DIFFRACTION3A967 - 1033
4X-RAY DIFFRACTION4A1034 - 1085
5X-RAY DIFFRACTION5A1086 - 1131
6X-RAY DIFFRACTION6A1132 - 1171
7X-RAY DIFFRACTION7A1172 - 1223
8X-RAY DIFFRACTION8A1224 - 1246
9X-RAY DIFFRACTION9A1247 - 1287
10X-RAY DIFFRACTION10A1288 - 1297

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