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- PDB-4isq: Binding domain of Botulinum neurotoxin DC in complex with human s... -

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Basic information

Entry
Database: PDB / ID: 4isq
TitleBinding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I
Components
  • Neurotoxin
  • Synaptotagmin-1
KeywordsTOXIN / Membrane binding / Synaptotagmin and Ganglioside binding
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Toxicity of botulinum toxin type B (botB) ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / chromaffin granule membrane / dense core granule / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / vesicle docking / exocytic vesicle / regulation of exocytosis / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle organization / protein heterooligomerization / vesicle fusion / positive regulation of dopamine secretion / Glutamate Neurotransmitter Release Cycle / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / syntaxin-1 binding / Neurexins and neuroligins / clathrin binding / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / presynaptic active zone / postsynaptic cytosol / excitatory synapse / protein transmembrane transporter activity / detection of calcium ion / positive regulation of synaptic transmission / presynaptic cytosol / regulation of synaptic transmission, glutamatergic / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / SNARE binding / hippocampal mossy fiber to CA3 synapse / clathrin-coated endocytic vesicle membrane / molecular condensate scaffold activity / metalloendopeptidase activity / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / toxin activity / chemical synaptic transmission / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / lipid binding / calcium ion binding / glutamatergic synapse / Golgi apparatus / proteolysis / extracellular region / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / 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 ...Synaptotagmin / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptotagmin-1 / Neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsBerntsson, R.P.-A. / Peng, L. / Svensson, L.M. / Dong, M. / Stenmark, P.
CitationJournal: Structure / Year: 2013
Title: Crystal Structures of Botulinum Neurotoxin DC in Complex with Its Protein Receptors Synaptotagmin I and II.
Authors: Berntsson, R.P. / Peng, L. / Svensson, L.M. / Dong, M. / Stenmark, P.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurotoxin
B: Neurotoxin
C: Neurotoxin
D: Synaptotagmin-1
E: Synaptotagmin-1
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,27034
Polymers157,6126
Non-polymers2,65828
Water4,738263
1
A: Neurotoxin
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,48212
Polymers52,5372
Non-polymers94510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-79 kcal/mol
Surface area19490 Å2
MethodPISA
2
B: Neurotoxin
E: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2069
Polymers52,5372
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-78 kcal/mol
Surface area19270 Å2
MethodPISA
3
C: Neurotoxin
D: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,58213
Polymers52,5372
Non-polymers1,04511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-111 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.227, 57.550, 165.274
Angle α, β, γ (deg.)90.000, 118.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neurotoxin


Mass: 50065.379 Da / Num. of mol.: 3 / Fragment: Hc domain (unp residues 864-1285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LBR1
#2: Protein/peptide Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 2471.825 Da / Num. of mol.: 3 / Fragment: toxin binding site (unp residues 33-53) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21579
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 4.37 Å3/Da / Density % sol: 71.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→48.5 Å / Num. all: 80170 / Num. obs: 80166 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.125 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.793.70.6581.142411115550.658100
2.79-2.963.60.4781.639195109800.47899.9
2.96-3.173.40.32.435437103490.399.9
3.17-3.423.70.1933.73569296530.193100
3.42-3.753.60.1235.73207788660.123100
3.75-4.193.40.0798.82760180910.079100
4.19-4.843.70.06111.52641271600.061100
4.84-5.933.50.06211.22091560440.062100
5.93-8.383.60.06511.11694547640.065100
8.38-48.5953.30.03419.1889227040.03499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.47 Å48.59 Å
Translation9.47 Å48.59 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→48.65 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.1996 / WRfactor Rwork: 0.1816 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8645 / SU B: 16.041 / SU ML: 0.171 / SU R Cruickshank DPI: 0.3221 / SU Rfree: 0.2259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 4003 5 %RANDOM
Rwork0.2036 ---
obs0.2045 80151 99.8 %-
all-80166 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.14 Å2 / Biso mean: 46.6984 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.47 Å2
2---4.26 Å2-0 Å2
3---2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10534 0 148 263 10945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0210960
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210127
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.9514818
X-RAY DIFFRACTIONr_angle_other_deg0.616323251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95951283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19525.099557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.568151917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0781542
X-RAY DIFFRACTIONr_chiral_restr0.0530.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022678
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 285 -
Rwork0.317 5596 -
all-5881 -
obs--99.75 %
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)
15.43880.9389-1.28434.08920.14463.8250.1356-0.0137-0.39920.19890.027-0.34530.33850.1741-0.16250.05390.033-0.03060.0448-0.00030.2557-76.8069-6.67218.5776
29.2933-5.6878-3.5196.2684-2.63599.57210.49881.03730.1519-0.4124-1.3297-0.64560.05540.82990.83090.35920.0355-0.22590.4067-0.04020.8331-63.62334.4723211.2519
32.45710.2980.48881.28320.54960.9686-0.0018-0.08380.24520.1124-0.0364-0.1318-0.08760.0450.03820.0734-0.01350.04140.14290.0130.2144-81.11511.972220.1461
44.48481.25480.35942.67260.19782.25120.0369-0.0250.10890.16640.0626-0.1236-0.33390.0482-0.09960.0720.02330.00160.0901-0.00170.2378-75.59496.8098219.2738
51.7488-0.1912-0.05341.10630.12320.3507-0.01020.06540.0106-0.0832-0.0015-0.0069-0.01570.01660.01170.1419-0.0110.05410.16980.01410.1082-112.1770.3345211.4043
64.445-0.43021.76394.7793-1.85993.73190.01310.122-0.6089-0.5560.20190.14450.95380.2112-0.21490.54160.0894-0.17470.0968-0.0620.2308-53.134513.2001183.8894
70.59451.6794-0.66354.9856-2.27221.4761-0.47010.43770.1702-0.92910.84170.48240.38220.1869-0.37170.7899-0.0379-0.31891.0852-0.06860.145-57.476720.9292172.6257
82.7840.24041.95612.6516-0.54923.6395-0.10560.55290.1597-0.42850.01280.0679-0.05440.40120.09280.11460.0111-0.04720.20260.04770.0582-49.171631.6436184.7301
92.9801-0.05491.63213.4106-0.19664.74190.14160.61230.2131-0.4761-0.05170.21640.20590.1862-0.08990.15080.0278-0.0760.16470.03380.0815-52.950428.3728181.9497
101.22140.44490.36621.10570.19281.28930.00410.03320.0418-0.0559-0.01230.1106-0.0317-0.04490.00820.10870.01190.00320.15090.00280.1702-43.528321.8855217.6332
118.79881.84655.10887.11324.34948.9239-0.4384-0.1778-0.21410.1420.07290.06520.39880.44360.36550.26680.06990.15320.10250.06970.0992-88.801-26.8502188.1095
122.1117-0.0172-1.07141.7938-0.08443.1503-0.0517-0.1038-0.19060.13870.02480.3646-0.0082-0.26230.02690.21190.02750.09580.1736-0.00520.1191-94.2773-17.5143182.3166
132.3117-0.47930.35522.77410.09964.2310.1007-0.32320.20530.2583-0.12620.2815-0.7584-0.1350.02550.3177-0.00280.12650.1043-0.0350.1049-89.4989-5.0776180.5276
140.5930.0882-0.94520.27380.24572.6833-0.0179-0.08410.05760.05720.01980.1197-0.0432-0.0288-0.00190.19320.00490.04990.1621-0.01850.1117-83.6727-18.7073165.8598
151.0516-0.1882-0.42141.637-0.16872.17390.0332-0.0455-0.01340.03750.0161-0.1746-0.01820.1406-0.04920.14240.00360.04250.1555-0.01410.0951-68.7197-19.8765149.6696
1618.60247.07433.65472.85850.691626.22020.7813-2.2923-1.03740.2445-1.1384-0.75020.21063.17210.35710.26650.0063-0.06351.25910.35571.0995-50.0052-21.1705149.6308
174.29311.9751.692715.72310.5360.6879-0.29660.1576-0.16330.42170.4078-1.1687-0.16050.0189-0.11120.3080.02520.01280.3280.04040.4336-55.8006-19.8223139.4023
1817.98985.754711.012811.2843-3.472111.93890.907-2.94861.14360.76190.02322.51880.2747-2.5082-0.93020.3592-0.00170.18070.78490.14010.7171-56.048420.9909237.0576
1911.4655-11.9401-4.138323.95255.13571.55850.28870.135-0.73350.4562-0.66042.0824-0.0709-0.05420.37160.2242-0.049-0.00080.3223-0.02140.3635-44.838322.0849239.2825
2024.38525.239-17.622110.6183.732518.7132-1.12593.2076-0.5953-2.09911.5908-1.2007-0.6746-1.6514-0.4650.6373-0.36060.13160.7211-0.1840.4722-122.5323-0.9733191.3088
210.21361.7624-0.762521.9128-13.52339.8439-0.242-0.0550.028-2.1452-0.3165-0.50130.98640.10490.55850.41340.03540.06480.3063-0.02010.2589-130.38690.5442200.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A863 - 918
2X-RAY DIFFRACTION2A919 - 935
3X-RAY DIFFRACTION3A936 - 1029
4X-RAY DIFFRACTION4A1030 - 1079
5X-RAY DIFFRACTION5A1080 - 1284
6X-RAY DIFFRACTION6B863 - 913
7X-RAY DIFFRACTION7B914 - 931
8X-RAY DIFFRACTION8B932 - 1020
9X-RAY DIFFRACTION9B1021 - 1077
10X-RAY DIFFRACTION10B1078 - 1284
11X-RAY DIFFRACTION11C863 - 896
12X-RAY DIFFRACTION12C897 - 969
13X-RAY DIFFRACTION13C970 - 1036
14X-RAY DIFFRACTION14C1037 - 1151
15X-RAY DIFFRACTION15C1152 - 1284
16X-RAY DIFFRACTION16D43 - 47
17X-RAY DIFFRACTION17D48 - 57
18X-RAY DIFFRACTION18E43 - 47
19X-RAY DIFFRACTION19E48 - 57
20X-RAY DIFFRACTION20F43 - 47
21X-RAY DIFFRACTION21F48 - 57

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