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- PDB-7t5f: Botulinum neurotoxin Type B Light Chain complexed with nanobodies... -

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Basic information

Entry
Database: PDB / ID: 7t5f
TitleBotulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10
Components
  • Botulinum neurotoxin type B
  • JLJ-G3
  • JNE-B10
KeywordsTOXIN / Botulinum neurotoxin / camelid heavy chain antibody / endopeptidase / inhibitor
Function / homology
Function and homology information


Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / 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
IODIDE ION / Botulinum neurotoxin type B
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJin, R. / Lam, K.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI125704 United States
CitationJournal: Plos Pathog. / Year: 2022
Title: Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies.
Authors: Lam, K.H. / Tremblay, J.M. / Perry, K. / Ichtchenko, K. / Shoemaker, C.B. / Jin, R.
History
DepositionDec 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
D: Botulinum neurotoxin type B
C: JLJ-G3
B: JNE-B10
E: JNE-B10
F: JLJ-G3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,09014
Polymers155,1976
Non-polymers8928
Water2,342130
1
A: Botulinum neurotoxin type B
C: JLJ-G3
B: JNE-B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1728
Polymers77,5993
Non-polymers5735
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Botulinum neurotoxin type B
E: JNE-B10
F: JLJ-G3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9186
Polymers77,5993
Non-polymers3193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.320, 88.276, 114.481
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

DetailsTrimer confirmed by gel filtration

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B


Mass: 49553.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli (E. coli) / References: UniProt: P10844, bontoxilysin

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Antibody , 2 types, 4 molecules CFBE

#2: Antibody JLJ-G3


Mass: 13940.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Antibody JNE-B10


Mass: 14104.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 138 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / References: bontoxilysin
#5: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.2 M KI, 0.1 M MES pH 6.5, 25 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→75.841 Å / Num. obs: 45137 / % possible obs: 99.2 % / Redundancy: 2.3 % / CC1/2: 0.99 / Net I/σ(I): 8.2
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 4493 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LcB

Resolution: 2.6→75.841 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 2280 5.05 %Random selection
Rwork0.194 ---
obs0.1955 45121 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→75.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10329 0 8 130 10467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110547
X-RAY DIFFRACTIONf_angle_d1.27714234
X-RAY DIFFRACTIONf_dihedral_angle_d13.933958
X-RAY DIFFRACTIONf_chiral_restr0.0571530
X-RAY DIFFRACTIONf_plane_restr0.0071853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65660.31711310.28012656X-RAY DIFFRACTION99
2.6566-2.71840.27711580.25832710X-RAY DIFFRACTION99
2.7184-2.78630.27351580.25352642X-RAY DIFFRACTION100
2.7863-2.86170.29311300.23712663X-RAY DIFFRACTION100
2.8617-2.94590.31141170.2372731X-RAY DIFFRACTION100
2.9459-3.0410.27881260.22562677X-RAY DIFFRACTION99
3.041-3.14970.25221320.22432694X-RAY DIFFRACTION99
3.1497-3.27580.24841420.22242695X-RAY DIFFRACTION99
3.2758-3.42490.22881420.20722660X-RAY DIFFRACTION99
3.4249-3.60540.27091440.19282685X-RAY DIFFRACTION99
3.6054-3.83130.22031470.18332669X-RAY DIFFRACTION99
3.8313-4.12710.20971550.17672665X-RAY DIFFRACTION99
4.1271-4.54240.1641410.16122661X-RAY DIFFRACTION98
4.5424-5.19960.16451470.15562668X-RAY DIFFRACTION98
5.1996-6.55030.2391570.19182663X-RAY DIFFRACTION98
6.5503-75.8410.17171530.16822702X-RAY DIFFRACTION97
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)
11.29850.1735-0.221.7875-0.05560.88360.01440.06810.10520.09340.03190.075-0.0631-0.0616-0.040.1984-0.00230.02120.24060.01940.165314.1473-22.020452.4045
20.3978-0.17030.112.01280.56730.5964-0.15610.160.1796-0.19570.2776-0.7219-0.09120.2574-0.10920.3097-0.0550.07070.43460.03540.419634.9668-13.907344.4775
32.41440.7191-0.83861.4398-0.81330.59740.1960.289-0.2432-0.3648-0.00430.0449-0.0131-0.0338-0.11390.3906-0.02710.05870.5056-0.07970.227121.437-40.063137.2187
40.8697-0.0018-0.12411.39440.41620.4553-0.07380.42710.1682-0.29890.1847-0.13720.03360.0405-0.09060.4116-0.05550.060.47870.01670.209926.1359-20.278837.3066
54.21521.2970.36943.08790.91741.446-0.09650.48180.8247-0.37790.12820.1716-0.2895-0.1595-0.0680.3952-0.00340.07190.27260.1030.466820.99324.300244.5302
60.61830.1930.17952.4967-0.00050.4619-0.0383-0.1391-0.2047-0.13430.10581.22690.1083-0.1519-0.05280.3098-0.003-0.06080.36310.09510.735719.7352.51914.7831
72.05030.0522-0.37163.06570.53070.4596-0.19750.1180.4474-0.4319-0.02721.2025-0.22-0.18970.08150.1806-0.053-0.14530.27340.10481.096411.334712.72342.6566
80.7105-0.3937-0.36872.31820.49420.9695-0.0611-0.1777-0.19890.13370.23140.26630.00780.045-0.08910.21520.00430.00820.25960.03510.243833.646-3.38587.6203
92.2259-1.0855-0.35123.1633-0.17781.2735-0.1837-0.1584-0.06950.24820.1248-0.56370.07440.1969-0.09480.30080.0322-0.02360.34830.00120.363945.67381.030712.3826
102.4504-0.55360.96981.1628-0.97071.4773-0.1663-0.44980.2360.59470.23960.2304-0.2946-0.3134-0.07950.62930.12040.09620.4965-0.01990.302929.767619.762923.0587
112.79180.26020.40122.70520.26851.83480.1415-0.2304-0.50540.38780.10540.4870.08590.0018-0.26470.35720.03430.05510.31450.09470.390430.6216-17.303312.0337
124.4066-0.638-0.33172.1895-1.13270.73640.07840.4789-0.5802-0.57180.15470.43450.4122-0.0174-0.18290.5031-0.0902-0.03020.382-0.0870.461.9442-59.421147.5698
134.4111-1.1237-3.31948.00921.73478.5633-0.0896-0.13540.1142-0.18130.2835-0.4607-0.23390.4187-0.20270.4198-0.0386-0.05970.4204-0.04130.30651.6387-48.597848.5118
141.54350.32580.05181.1656-0.21071.0526-0.1420.4306-0.3859-0.25870.2524-0.02690.1143-0.3234-0.08920.3991-0.0459-0.03120.4477-0.02060.31570.5477-57.580648.0036
153.0429-3.3118-1.5913.71982.33764.00180.2578-0.29530.45010.0083-0.0109-0.1681-0.42250.4098-0.23160.6090.02390.05090.30790.01840.317214.5044-18.923281.92
160.54810.2213-0.26591.5022-0.26081.760.2083-0.313-0.00110.5262-0.07160.335-0.1953-0.0222-0.21440.5369-0.0590.11810.43790.02320.3033.5602-25.758578.6513
174.29063.3923-1.61497.1143-2.88033.86680.0212-0.127-0.38360.0161-0.01290.24490.1231-0.48180.06910.3743-0.07260.13650.40530.02640.4634-3.3289-28.122874.2994
184.11893.2854-1.697.7823-3.42975.31260.3399-0.52010.21130.8881-0.41190.5334-0.584-0.1327-0.04290.5209-0.06520.15120.4391-0.02440.28761.6634-17.53577.4045
196.15980.9771-1.57190.2412-0.46881.10470.1831-0.1493-0.35080.47220.0090.40440.3395-0.5087-0.15840.7133-0.15370.19010.59390.0820.4789-0.1965-30.717184.4156
203.2825-0.2606-2.37031.1130.1734.07550.1373-0.403-0.0610.8953-0.21220.19130.12260.07490.1350.6914-0.04060.01280.4257-0.00330.38838.531-29.369180.2635
216.32453.56055.24372.69062.3165.73690.15580.4731-0.2163-0.1370.0192-0.00710.11750.304-0.07151.0973-0.2913-0.50410.47280.10030.861420.80931.0243-25.7652
222.3543-0.15881.52570.0122-0.1241.09320.001-0.1490.2036-0.2065-0.09130.2437-0.0825-0.29120.06091.1702-0.1447-0.90950.7325-0.1871.17735.46024.9537-30.6173
232.71780.4732-0.97590.6470.12420.50.01030.64370.2275-0.5251-0.13260.5291-0.3161-0.23610.25030.9249-0.1294-0.92410.56050.24920.982816.36585.3774-17.5987
242.1237-0.30510.72310.6674-0.61.34750.05030.33490.0908-0.4628-0.07660.5827-0.2635-0.16690.14160.64720.1268-1.32350.49190.15371.60266.81710.0625-16.6064
250.823-0.42681.40044.3329-2.46154.48280.03390.0076-0.2518-0.3904-0.03280.5528-0.1149-0.4555-0.27291.01080.0778-0.78730.65210.07521.32358.0830.4548-21.2805
266.4666-2.98422.89471.6179-2.11373.7808-0.00771.08130.5403-0.2041-0.29110.0569-0.17270.02650.21821.2368-0.0441-0.80210.64520.02791.08748.682713.1048-28.4229
273.27010.31842.56520.1009-0.21625.0870.15790.32820.0112-0.49460.13170.2367-0.0842-0.0634-0.14511.2379-0.3529-0.59760.61720.26751.053717.024911.164-22.9994
282.49182.4779-0.37293.6018-1.22531.96850.1849-0.97720.99190.4543-0.09240.6348-0.7927-0.3842-0.25870.66490.28-0.04410.5893-0.06430.53213.749446.124911.1828
292.31420.461-0.7693.22950.2981.1501-0.1361-0.7228-0.15250.18690.07010.25050.03610.08310.15440.42270.14620.0360.54850.01860.495211.45437.64158.4363
302.5336-0.0724-0.28653.8788-2.42837.3648-0.2862-0.3325-0.56590.2480.2183-0.0208-0.0003-0.38680.17810.38430.05110.10650.45160.03840.43744.879635.91054.0959
314.8346-0.4608-0.36121.210.38720.322-0.3961-1.1610.17210.34440.2851-0.0302-0.1804-0.68370.13860.44040.2516-0.02620.88530.0330.40659.623440.14613.1229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 206 )
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 281 )
3X-RAY DIFFRACTION3chain 'A' and (resid 282 through 327 )
4X-RAY DIFFRACTION4chain 'A' and (resid 328 through 388 )
5X-RAY DIFFRACTION5chain 'A' and (resid 389 through 425 )
6X-RAY DIFFRACTION6chain 'D' and (resid 2 through 134 )
7X-RAY DIFFRACTION7chain 'D' and (resid 135 through 161 )
8X-RAY DIFFRACTION8chain 'D' and (resid 162 through 239 )
9X-RAY DIFFRACTION9chain 'D' and (resid 240 through 281 )
10X-RAY DIFFRACTION10chain 'D' and (resid 282 through 354 )
11X-RAY DIFFRACTION11chain 'D' and (resid 355 through 425 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 44 )
13X-RAY DIFFRACTION13chain 'C' and (resid 45 through 63 )
14X-RAY DIFFRACTION14chain 'C' and (resid 64 through 116 )
15X-RAY DIFFRACTION15chain 'B' and (resid 0 through 7 )
16X-RAY DIFFRACTION16chain 'B' and (resid 8 through 57 )
17X-RAY DIFFRACTION17chain 'B' and (resid 58 through 73 )
18X-RAY DIFFRACTION18chain 'B' and (resid 74 through 83 )
19X-RAY DIFFRACTION19chain 'B' and (resid 84 through 98 )
20X-RAY DIFFRACTION20chain 'B' and (resid 99 through 116 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 7 )
22X-RAY DIFFRACTION22chain 'E' and (resid 8 through 25 )
23X-RAY DIFFRACTION23chain 'E' and (resid 26 through 39 )
24X-RAY DIFFRACTION24chain 'E' and (resid 45 through 73 )
25X-RAY DIFFRACTION25chain 'E' and (resid 74 through 84 )
26X-RAY DIFFRACTION26chain 'E' and (resid 85 through 98 )
27X-RAY DIFFRACTION27chain 'E' and (resid 99 through 115 )
28X-RAY DIFFRACTION28chain 'F' and (resid 2 through 17 )
29X-RAY DIFFRACTION29chain 'F' and (resid 18 through 52 )
30X-RAY DIFFRACTION30chain 'F' and (resid 53 through 82 )
31X-RAY DIFFRACTION31chain 'F' and (resid 83 through 116 )

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