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- PDB-2np0: Crystal structure of the Botulinum neurotoxin type B complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2np0
TitleCrystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain
Components
  • Botulinum neurotoxin type B
  • Synaptotagmin-2
KeywordsHYDROLASE / BOTULINUM / NEUROTOXIN / SYNAPTOTAGAMIN / RECEPTOR
Function / homology
Function and homology information


calcium-dependent activation of synaptic vesicle fusion / Toxicity of botulinum toxin type B (botB) / chromaffin granule membrane / inositol 1,3,4,5 tetrakisphosphate binding / dense core granule / calcium ion-regulated exocytosis of neurotransmitter / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / bontoxilysin ...calcium-dependent activation of synaptic vesicle fusion / Toxicity of botulinum toxin type B (botB) / chromaffin granule membrane / inositol 1,3,4,5 tetrakisphosphate binding / dense core granule / calcium ion-regulated exocytosis of neurotransmitter / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / calcium-dependent phospholipid binding / syntaxin binding / host cell cytosol / clathrin binding / phosphatidylserine binding / protein transmembrane transporter activity / synaptic vesicle endocytosis / SNARE binding / neuromuscular junction / metalloendopeptidase activity / synaptic vesicle membrane / toxin activity / cell differentiation / axon / lipid binding / calcium ion binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Synaptotagmin / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain ...Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Synaptotagmin / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / C2 domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Alpha-Beta Complex / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type B / Synaptotagmin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Clostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsChai, Q. / Arndt, J.W. / Stevens, R.C.
CitationJournal: Nature / Year: 2006
Title: Structural basis of cell surface receptor recognition by botulinum neurotoxin B.
Authors: Chai, Q. / Arndt, J.W. / Dong, M. / Tepp, W.H. / Johnson, E.A. / Chapman, E.R. / Stevens, R.C.
History
DepositionOct 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
B: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,5917
Polymers153,3702
Non-polymers2215
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-88 kcal/mol
Surface area55440 Å2
MethodPISA
2
A: Botulinum neurotoxin type B
B: Synaptotagmin-2
hetero molecules

A: Botulinum neurotoxin type B
B: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,18314
Polymers306,7404
Non-polymers44210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5560 Å2
ΔGint-189 kcal/mol
Surface area108780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.415, 351.971, 101.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Botulinum neurotoxin type B


Mass: 150833.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: Type B1_Okra / References: UniProt: P10844, bontoxilysin
#2: Protein/peptide Synaptotagmin-2 / Synaptotagmin II / SytII


Mass: 2536.852 Da / Num. of mol.: 1 / Fragment: Vesicular (Residues 1-60)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt2 / References: UniProt: P46097

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Non-polymers , 4 types, 411 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.98 Å3/Da / Density % sol: 75.32 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: Double crystal, paralell (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→40 Å / Num. obs: 92718 / % possible obs: 90.04 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.62→2.71 Å / Rmerge(I) obs: 0.476 / % possible all: 71

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s0e

1s0e


Resolution: 2.62→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.896 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.293 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22733 4177 5 %RANDOM
Rwork0.18601 ---
all0.1881 79045 --
obs0.18807 83222 90.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.371 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å20 Å20 Å2
2---1.75 Å20 Å2
3----3.47 Å2
Refinement stepCycle: LAST / Resolution: 2.62→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10771 0 5 406 11182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211006
X-RAY DIFFRACTIONr_bond_other_d0.0010.027542
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.95414861
X-RAY DIFFRACTIONr_angle_other_deg0.934318434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.51251301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63225.464571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.645152029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4641538
X-RAY DIFFRACTIONr_chiral_restr0.1160.21600
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022228
X-RAY DIFFRACTIONr_nbd_refined0.2230.22280
X-RAY DIFFRACTIONr_nbd_other0.1940.27802
X-RAY DIFFRACTIONr_nbtor_refined0.1980.25479
X-RAY DIFFRACTIONr_nbtor_other0.0910.26024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2449
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.211
X-RAY DIFFRACTIONr_mcbond_it0.6261.56745
X-RAY DIFFRACTIONr_mcbond_other0.0941.52627
X-RAY DIFFRACTIONr_mcangle_it1.05210584
X-RAY DIFFRACTIONr_scbond_it1.45235012
X-RAY DIFFRACTIONr_scangle_it2.2744.54277
LS refinement shellResolution: 2.62→2.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 236 -
Rwork0.371 4553 -
obs--70.96 %
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)
10.78370.3557-0.02241.95110.19221.1674-0.0597-0.0753-0.15660.107-0.01010.12530.009-0.19240.0698-0.19660.04880.0253-0.19540.0341-0.151166.56228.8852-6.0405
20.5713-0.0681-0.43231.4964-0.27951.0801-0.07290.1091-0.1522-0.33730.06090.1481-0.1606-0.24040.012-0.0320.1184-0.0088-0.08780.0239-0.144169.543447.3429-14.5235
30.8748-0.2089-0.02661.0630.61441.339-0.0552-0.03480.0634-0.04280.00820.0466-0.3852-0.24340.0469-0.13760.099-0.0216-0.18990.0353-0.223667.275260.7491-0.6559
42.3507-0.0929-0.34952.87430.87753.33870.01570.10510.1792-0.2837-0.0213-0.222-0.080.39080.0055-0.06890.11380.0155-0.14860.0713-0.161560.508493.9521-13.2184
53.36460.202-1.55822.8973-0.17783.72770.0263-0.49970.46080.35830.0713-0.01-0.2784-0.0132-0.09750.10480.1067-0.0483-0.1485-0.1258-0.112946.2825108.965614.6012
649.3135-3.617414.12635.155815.42747.891-0.3847-2.25330.35520.68490.0869-0.8613-1.1556-0.09580.29780.00040.0019-0.00010.0013-0.00020.000142.4767121.808329.4188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4371 - 437
2X-RAY DIFFRACTION2AA438 - 500438 - 500
3X-RAY DIFFRACTION3AA501 - 872501 - 872
4X-RAY DIFFRACTION4AA873 - 1090873 - 1090
5X-RAY DIFFRACTION5AA1091 - 12901091 - 1290
6X-RAY DIFFRACTION6BB45 - 596 - 20

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