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- PDB-4isr: Binding domain of Botulinum neurotoxin DC in complex with rat syn... -

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Basic information

Entry
Database: PDB / ID: 4isr
TitleBinding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II
Components
  • Neurotoxin
  • Synaptotagmin-2
KeywordsTOXIN / Membrane binding / Synaptotagmin and Ganglioside binding
Function / homology
Function and homology information


calcium-dependent activation of synaptic vesicle fusion / dense core granule / chromaffin granule membrane / inositol 1,3,4,5 tetrakisphosphate binding / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of dendrite extension ...calcium-dependent activation of synaptic vesicle fusion / dense core granule / chromaffin granule membrane / inositol 1,3,4,5 tetrakisphosphate binding / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / synaptic vesicle endocytosis / protein transmembrane transporter activity / cellular response to calcium ion / neuromuscular junction / terminal bouton / metalloendopeptidase activity / synaptic vesicle membrane / toxin activity / cell differentiation / axon / calcium ion binding / proteolysis / zinc ion binding / extracellular region / plasma membrane
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 N-terminal / Clostridium neurotoxin, receptor-binding C-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 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / C2 domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptotagmin-2 / Neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 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 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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-2
E: Synaptotagmin-2
F: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,91718
Polymers157,7656
Non-polymers1,15312
Water7,746430
1
A: Neurotoxin
D: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9726
Polymers52,5882
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-56 kcal/mol
Surface area19950 Å2
MethodPISA
2
B: Neurotoxin
E: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0697
Polymers52,5882
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-74 kcal/mol
Surface area19680 Å2
MethodPISA
3
C: Neurotoxin
F: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8765
Polymers52,5882
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-46 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.244, 57.781, 169.555
Angle α, β, γ (deg.)90.000, 118.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C
14D
24E
15D
25F
16E
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERAA863 - 128410 - 431
21SERSERSERSERBB863 - 128410 - 431
12ILEILEALAALAAA864 - 128311 - 430
22ILEILEALAALACC864 - 128311 - 430
13ILEILESERSERBB864 - 128411 - 431
23ILEILESERSERCC864 - 128411 - 431
14SERSERGLUGLUDD42 - 573 - 18
24SERSERGLUGLUEE42 - 573 - 18
15SERSERGLUGLUDD42 - 573 - 18
25SERSERGLUGLUFF42 - 573 - 18
16SERSERGLUGLUEE42 - 573 - 18
26SERSERGLUGLUFF42 - 573 - 18

NCS ensembles :
ID
1
2
3
4
5
6

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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-2 / / Synaptotagmin II / SytII


Mass: 2522.826 Da / Num. of mol.: 3 / Fragment: toxin binding site (unp residues 40-60) / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P29101
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 4.51 Å3/Da / Density % sol: 72.72 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.95 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.59→47.733 Å / Num. all: 88992 / Num. obs: 88514 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.489 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.59-2.740.6312.32556761406298.5
2.74-2.930.4053.62532781329699.8
2.93-3.170.2376.02498851246199.8
3.17-3.470.13310.35458811146799.8
3.47-3.880.08715.3417521045699.8
3.88-4.470.05721.7836747923999.8
4.47-5.460.04924.5230932782199.7
5.46-7.680.05820.8424080614999.6
7.680.02834.9413181356397.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.54 Å47.73 Å
Translation2.54 Å47.73 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→47.73 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2052 / WRfactor Rwork: 0.1933 / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8668 / SU B: 13.772 / SU ML: 0.149 / SU R Cruickshank DPI: 0.3047 / SU Rfree: 0.2243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 4426 5 %RANDOM
Rwork0.2196 ---
obs0.2204 88514 99.61 %-
all-88992 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 40.9719 Å2 / Biso min: 3.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å21.53 Å2
2---3.45 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.59→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10554 0 60 430 11044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0210847
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.93814668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3151281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18125.027557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.521151904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0841542
X-RAY DIFFRACTIONr_chiral_restr0.0670.21575
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028235
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A5040.04
12B5040.04
21A5210.09
22C5210.09
31B5120.07
32C5120.07
41D170.14
42E170.14
51D140.15
52F140.15
61E140.15
62F140.15
LS refinement shellResolution: 2.588→2.655 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 316 -
Rwork0.297 6001 -
all-6317 -
obs--96.8 %
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)
17.05141.07172.06884.5475-0.33042.9815-0.01350.1710.65630.13130.10090.2793-0.46460.0434-0.08740.09730.01770.01680.0496-0.03740.30361.613710.088173.5355
23.70652.5993-0.28713.33071.41913.57550.19330.49570.497-0.091-0.09010.54780.19-0.7391-0.10320.16350.0046-0.08090.30850.07020.3447-3.583-1.181968.1187
34.01471.0520.82580.971-0.16280.55620.2042-0.3304-0.26630.1349-0.1481-0.11670.0539-0.0158-0.05610.0772-0.0247-0.04570.21010.0150.24526.394-8.491479.0553
43.80770.6273-0.96921.96930.00252.07510.00530.0496-0.15440.105-0.02840.010.1822-0.03640.02310.0238-0.0044-0.01660.1335-0.00010.2332.2874-6.217172.8723
52.3564-0.00810.03440.3511-0.16950.249-0.03520.10670.0391-0.03110.0086-0.03220.0117-0.03780.02670.097-0.0051-0.04020.1668-0.01110.2132.92344.554268.7464
62.1342-0.2743-0.10661.772-0.45970.5477-0.03660.1649-0.1539-0.18250.0187-0.0236-0.0159-0.03850.0180.0845-0.0089-0.01640.1771-0.03920.174341.59871.053863.9079
712.1438-5.6347-0.80239.9327-0.70312.6855-0.1680.04630.6215-0.28630.4764-0.6392-0.57790.0421-0.30840.3958-0.1990.1270.2445-0.01770.1132-16.2553-11.609436.6616
87.4143.4283-1.49642.489-0.37195.7973-0.52280.52660.4591-0.46950.25410.454-0.0711-0.63540.26870.27620.0156-0.03390.24030.09870.1699-26.694-13.50936.6101
93.65830.7477-1.22632.15050.7573.6306-0.28630.3263-0.0463-0.58640.28890.0494-0.0806-0.2941-0.00260.2345-0.08330.03370.25090.01320.0352-25.8984-25.592139.7146
102.7190.5706-1.34312.2467-0.43772.4918-0.49340.3789-0.3334-0.40910.2081-0.06120.4465-0.1820.28530.2688-0.14430.13380.2476-0.11710.0963-23.1495-32.381139.3124
110.65470.1219-1.31912.04871.81044.7924-0.12710.09520.0396-0.29740.1993-0.0327-0.0702-0.0123-0.07210.1763-0.04960.03510.23620.01370.1357-23.4045-19.252448.768
120.91510.3942-0.58761.1195-0.37580.96750.0526-0.03820.03420.0267-0.03650.0457-0.0359-0.0611-0.01610.09520.0019-0.00250.1688-0.00010.1729-35.5437-16.004875.0438
130.92160.85-0.69231.6719-0.36691.4766-0.0631-0.028-0.06150.00520.0085-0.17350.10950.06790.05460.0830.0209-0.00250.18040.00550.1876-30.3424-23.206477.469
144.4202-1.78050.31356.3905-2.33174.1318-0.3519-0.86060.83770.7340.3813-0.7026-0.99310.0835-0.02940.5701-0.0449-0.18210.4343-0.2170.271817.976525.620239.2762
152.8351-1.26671.22812.11860.086.23310.0225-0.1812-0.0230.09970.0583-0.19460.66850.502-0.08070.2730.092-0.07340.34230.02590.048818.92059.876330.365
162.0355-0.32641.52791.35790.78165.5127-0.0646-0.491-0.03080.36950.1867-0.26310.50430.0608-0.12210.3520.0675-0.1310.3780.02520.081916.576411.219436.6991
171.4349-0.00340.52180.3409-0.04060.7658-0.0328-0.2623-0.08340.0340.0391-0.0020.0519-0.0118-0.00630.28620.020.03180.2380.02310.03561.808118.793417.3875
182.1482-0.5733-1.14864.56091.20093.38920.0661-0.3160.32830.14780.131-0.2456-0.34820.2729-0.19710.2555-0.0388-0.02820.1908-0.02350.06451.045426.431111.1446
191.093-0.51660.55592.24660.20341.72640.0569-0.02720.00160.1004-0.00330.21080.0742-0.1107-0.05370.1694-0.010.03150.17770.00920.0813-8.942119.46473.3374
2017.970.274911.94899.46731.386418.69290.23151.63650.2808-0.7226-0.2477-0.51790.92991.10010.01620.1859-0.02030.10430.2594-0.01820.141253.6094.191753.1786
2116.44042.3975-5.07078.72920.616111.87760.2837-1.2301-0.52060.6712-0.1201-0.296-0.1160.4593-0.16360.13680.0255-0.09580.1778-0.01970.1009-25.7957-18.089693.7753
226.6543-2.8253-3.56485.08142.644721.5806-0.24560.5751-0.0984-0.2182-0.21510.79240.0266-1.25570.46070.05680.0062-0.02630.21550.05120.2961-24.309321.3249-0.5635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A863 - 920
2X-RAY DIFFRACTION2A921 - 943
3X-RAY DIFFRACTION3A944 - 1003
4X-RAY DIFFRACTION4A1004 - 1072
5X-RAY DIFFRACTION5A1073 - 1196
6X-RAY DIFFRACTION6A1197 - 1284
7X-RAY DIFFRACTION7B863 - 892
8X-RAY DIFFRACTION8B893 - 927
9X-RAY DIFFRACTION9B928 - 958
10X-RAY DIFFRACTION10B959 - 1040
11X-RAY DIFFRACTION11B1041 - 1107
12X-RAY DIFFRACTION12B1108 - 1206
13X-RAY DIFFRACTION13B1207 - 1284
14X-RAY DIFFRACTION14C864 - 932
15X-RAY DIFFRACTION15C933 - 1003
16X-RAY DIFFRACTION16C1004 - 1072
17X-RAY DIFFRACTION17C1073 - 1131
18X-RAY DIFFRACTION18C1132 - 1163
19X-RAY DIFFRACTION19C1164 - 1284
20X-RAY DIFFRACTION20D42 - 57
21X-RAY DIFFRACTION21E42 - 57
22X-RAY DIFFRACTION22F42 - 57

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