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- PDB-6es1: Crystal structure of the binding domain from botulinum neurotoxin... -

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Basic information

Entry
Database: PDB / ID: 6es1
TitleCrystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C
Components
  • Botulinum neurotoxin type A
  • Synaptic vesicle glycoprotein 2C
KeywordsPROTEIN BINDING / Receptor / Human / Clostridium botulinum / Binding domain / SV2C
Function / homology
Function and homology information


Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type A (botA) / dopaminergic synapse / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / neurotransmitter transport / host cell cytosol / regulation of synaptic vesicle exocytosis ...Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type A (botA) / dopaminergic synapse / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / neurotransmitter transport / host cell cytosol / regulation of synaptic vesicle exocytosis / transmembrane transporter activity / protein transmembrane transporter activity / metalloendopeptidase activity / synaptic vesicle membrane / synaptic vesicle / toxin activity / chemical synaptic transmission / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Synaptic vesicle protein SV2 / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain ...Synaptic vesicle protein SV2 / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / 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 / Major facilitator superfamily / Major Facilitator Superfamily / Pectate Lyase C-like / Kunitz inhibitor STI-like superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / 3 Solenoid / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Botulinum neurotoxin type A2 / Synaptic vesicle glycoprotein 2C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGustafsson, R. / Masuyer, G. / Stenmark, P.
Funding support Sweden, United States, 4items
OrganizationGrant numberCountry
Swedish Research Council2014-5667 Sweden
Wenner-Gren Foundation Sweden
Swedish Cancer Society Sweden
National Institutes of Health1R01NS080833 United States
CitationJournal: Toxins (Basel) / Year: 2018
Title: Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding.
Authors: Gustafsson, R. / Zhang, S. / Masuyer, G. / Dong, M. / Stenmark, P.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Synaptic vesicle glycoprotein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5813
Polymers65,5222
Non-polymers591
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-3 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.714, 122.108, 47.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 51643.477 Da / Num. of mol.: 1 / Fragment: Binding domain, UNP residues 874-1296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45894, bontoxilysin
#2: Protein Synaptic vesicle glycoprotein 2C


Mass: 13878.354 Da / Num. of mol.: 1 / Fragment: luminal domain 4, UNP residues 474-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SV2C, KIAA1054 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1R / References: UniProt: Q496J9
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.919908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919908 Å / Relative weight: 1
ReflectionResolution: 2→47.66 Å / Num. obs: 40692 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.242 / Net I/σ(I): 9.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.237 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2897 / CC1/2: 0.481 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JRA chain C; 3BTA

4jra

3bta


Resolution: 2→47.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.605 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22967 2010 4.9 %RANDOM
Rwork0.18139 ---
obs0.18387 38627 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.539 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2---0.7 Å20 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 2→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 4 359 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024383
X-RAY DIFFRACTIONr_bond_other_d0.0020.023961
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9345924
X-RAY DIFFRACTIONr_angle_other_deg0.9639221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60225.044228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65815794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2711519
X-RAY DIFFRACTIONr_chiral_restr0.10.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.7072089
X-RAY DIFFRACTIONr_mcbond_other0.9591.7042087
X-RAY DIFFRACTIONr_mcangle_it1.6662.5492617
X-RAY DIFFRACTIONr_mcangle_other1.6652.5512618
X-RAY DIFFRACTIONr_scbond_it0.9791.8032294
X-RAY DIFFRACTIONr_scbond_other0.9791.8042295
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6332.6563308
X-RAY DIFFRACTIONr_long_range_B_refined4.75820.2375028
X-RAY DIFFRACTIONr_long_range_B_other4.75820.2445029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 114 -
Rwork0.29 2776 -
obs--97.6 %
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)
11.57731.19880.11492.34370.18480.9665-0.04450.07680.04790.07770.03160.2336-0.0201-0.04380.01290.03290.0073-0.00430.013800.0808-24.99144.8469-9.125
21.3551-0.11560.12091.321-0.64991.12980.0785-0.0150.1730.0708-0.0323-0.127-0.14140.0408-0.04620.0529-0.00840.01920.0221-0.03110.0883-5.773433.1336-16.646
31.5047-0.39340.12461.4537-0.48582.31090.09260.19970.1011-0.1804-0.0721-0.03620.16370.0358-0.02050.0490.0190.00290.0367-0.010.0649-5.059727.9557-25.7905
42.9429-2.54930.43565.4791.71622.4856-0.0225-0.3604-0.01350.78950.06180.50760.16770.3121-0.03930.3469-0.18470.19120.3533-0.18510.221911.178418.759619.2101
55.6904-0.1264-1.78085.309-0.33430.8149-0.0902-0.14090.14430.09630.2042-0.16360.01190.1696-0.1140.0793-0.0316-0.02910.1143-0.04620.045516.985319.660713.8374
64.5226-0.6826-0.16494.88890.17160.55460.0237-0.03130.1562-0.08690.0998-0.2971-0.04880.0835-0.12340.0534-0.0078-0.0020.0203-0.02440.049116.417919.60797.4459
71.40430.9308-0.52274.5496-1.0632.4494-0.0270.0164-0.0397-0.32510.12010.00590.12450.0341-0.09310.0381-0.0204-0.00730.0261-0.00910.020910.324517.02454.2642
80.9942-0.9431-0.03914.6056-0.49192.1701-0.02150.124-0.0793-0.20740.0636-0.02050.02990.0475-0.04210.0603-0.0185-0.01810.0277-0.01420.02510.260316.04430.0108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A876 - 1093
2X-RAY DIFFRACTION2A1094 - 1223
3X-RAY DIFFRACTION3A1224 - 1295
4X-RAY DIFFRACTION4B473 - 484
5X-RAY DIFFRACTION5B485 - 501
6X-RAY DIFFRACTION6B502 - 532
7X-RAY DIFFRACTION7B533 - 548
8X-RAY DIFFRACTION8B549 - 567

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