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- PDB-6dkk: Structure of BoNT -

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Basic information

Entry
Database: PDB / ID: 6dkk
TitleStructure of BoNT
ComponentsBotulinum neurotoxin type A
KeywordsTOXIN / Protein translocation / Botulinum neurotoxin
Function / homology
Function and homology information


host cell junction / Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity ...host cell junction / Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / 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 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 ...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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum A str. ATCC 19397 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091823 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125704 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI123920 United States
CitationJournal: Nat Commun / Year: 2018
Title: A viral-fusion-peptide-like molecular switch drives membrane insertion of botulinum neurotoxin A1.
Authors: Lam, K.H. / Guo, Z. / Krez, N. / Matsui, T. / Perry, K. / Weisemann, J. / Rummel, A. / Bowen, M.E. / Jin, R.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1023
Polymers75,0072
Non-polymers951
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-44 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.659, 167.659, 222.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 37503.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum A str. ATCC 19397 (bacteria)
Gene: botA, atx, bna / Production host: Escherichia coli (E. coli)
References: UniProt: P10845, UniProt: P0DPI0*PLUS, bontoxilysin
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 1.4 M sodium potassium phosphate and 0.1 M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.7→52.01 Å / Num. obs: 32915 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.8
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.609

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V0A

3v0a


Resolution: 2.7→52.01 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2234 1662 5.05 %
Rwork0.2091 --
obs0.2098 32906 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 5 27 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095244
X-RAY DIFFRACTIONf_angle_d1.1677110
X-RAY DIFFRACTIONf_dihedral_angle_d13.7751933
X-RAY DIFFRACTIONf_chiral_restr0.073820
X-RAY DIFFRACTIONf_plane_restr0.004899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.77950.36171450.34062537X-RAY DIFFRACTION99
2.7795-2.86920.31151240.29682605X-RAY DIFFRACTION99
2.8692-2.97170.2641440.27162597X-RAY DIFFRACTION100
2.9717-3.09070.28451300.25592590X-RAY DIFFRACTION100
3.0907-3.23140.26671310.25622609X-RAY DIFFRACTION100
3.2314-3.40170.26181330.22932600X-RAY DIFFRACTION99
3.4017-3.61480.2141350.21722566X-RAY DIFFRACTION98
3.6148-3.89380.1951290.19972598X-RAY DIFFRACTION99
3.8938-4.28550.18471460.18492613X-RAY DIFFRACTION99
4.2855-4.90520.17911570.16632621X-RAY DIFFRACTION100
4.9052-6.17840.22781540.21352583X-RAY DIFFRACTION98
6.1784-52.02130.23331340.18822725X-RAY DIFFRACTION99
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)
12.052-0.47710.97330.60880.98393.1595-0.0185-0.43750.01640.184-0.08330.1132-0.448-0.2938-00.8416-0.19890.14720.9055-0.13120.639729.467670.70628.3427
22.050.4552-0.97422.02850.28140.65480.188-0.4529-0.3688-0.3439-0.1878-0.562-0.17150.4224-0.00930.5570.00490.13910.69940.10970.707549.739553.9264-0.8075
31.1196-0.2405-1.46510.3129-0.59292.83360.0204-0.5691-0.3006-0.1034-0.0988-0.1989-0.33620.634-00.5412-0.26440.10920.9323-0.1010.913350.906161.437511.0778
42.0977-0.73420.91461.63420.28611.4977-0.2031-0.4054-0.14690.2443-0.0162-0.59690.80551.2224-0.00540.80930.44230.03471.41280.2140.942145.395135.595418.3585
51.5616-1.382-0.10072.56620.68931.1580.4958-0.59830.21850.2901-0.2398-0.0832-0.56710.392-00.5332-0.11110.06590.768-0.0520.45435.991661.434212.082
61.5553-0.7648-0.81721.55510.40761.50210.23380.0455-0.8234-0.0664-0.21690.55180.17850.0346-0.00760.4217-0.0018-0.02240.53740.03930.570512.784448.990511.5993
70.0364-0.0501-0.01780.0715-0.00820.0271-0.1989-1.5987-0.97230.78920.6660.5430.89041.1023-01.74960.4675-0.17941.80970.23111.095548.285319.975930.5318
85.9112-2.1751.90230.6765-0.66631.6845-0.5366-0.68350.23210.33380.3106-0.1901-0.1542-0.5191-00.5180.08710.0030.64270.02520.54565.231558.313315.5569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 545 through 619 )
2X-RAY DIFFRACTION2chain 'A' and (resid 620 through 720 )
3X-RAY DIFFRACTION3chain 'A' and (resid 721 through 857 )
4X-RAY DIFFRACTION4chain 'B' and (resid 545 through 618 )
5X-RAY DIFFRACTION5chain 'B' and (resid 619 through 657 )
6X-RAY DIFFRACTION6chain 'B' and (resid 658 through 751 )
7X-RAY DIFFRACTION7chain 'B' and (resid 752 through 773 )
8X-RAY DIFFRACTION8chain 'B' and (resid 774 through 870 )

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