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- PDB-6ul4: Crystal structure of BoNT/B receptor-binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ul4
TitleCrystal structure of BoNT/B receptor-binding domain in complex with VHH JLO-G11
Components
  • Botulinum neurotoxin type B
  • VHH JLO-G11
KeywordsTOXIN/ANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / receptor-binding domain / TOXIN / ANTITOXIN / TOXIN-ANTITOXIN complex
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 / extracellular region / zinc ion binding / membrane
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type B
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18424332787 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins
Authors: Lam, K. / Tremblay, J.M. / Vazquez-Cintron, E. / Perry, K. / Ondeck, C. / Webb, R. / McNutt, P.M. / Shoemaker, C.B. / Jin, R.
History
DepositionOct 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
B: VHH JLO-G11


Theoretical massNumber of molelcules
Total (without water)69,3732
Polymers69,3732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.299, 267.905, 144.693
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 52534.145 Da / Num. of mol.: 1 / Fragment: receptor-binding domain
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
#2: Antibody VHH JLO-G11


Mass: 16838.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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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: 4.2 Å3/Da / Density % sol: 70.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20 % Ethanol, 0.1 M Tris

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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 315 / Detector: CCD / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.18→144.69 Å / Num. obs: 18645 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 91.9898983607 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.138 / Net I/σ(I): 8.5
Reflection shellResolution: 3.18→3.4 Å / Num. unique obs: 3299 / CC1/2: 0.376 / Rpim(I) all: 1.682

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Processing

Software
NameVersionClassification
XDS1.9_1692data reduction
PHENIX1.9_1692refinement
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NM1

2nm1


Resolution: 3.18424332787→45.3790661812 Å / SU ML: 0.536173848637 / Cross valid method: FREE R-VALUE / σ(F): 1.33460837583 / Phase error: 28.5304948501
RfactorNum. reflection% reflection
Rfree0.258187196644 865 4.7126123672 %
Rwork0.204073441307 --
obs0.206496836949 18355 97.1369602032 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 99.6475023187 Å2
Refinement stepCycle: LAST / Resolution: 3.18424332787→45.3790661812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 0 0 4581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004025710070394709
X-RAY DIFFRACTIONf_angle_d0.8103396095326353
X-RAY DIFFRACTIONf_chiral_restr0.0412162891051657
X-RAY DIFFRACTIONf_plane_restr0.00327541480792815
X-RAY DIFFRACTIONf_dihedral_angle_d12.97876882431745
LS refinement shellResolution: 3.18424332787→3.3837 Å
RfactorNum. reflection% reflection
Rfree0.397676559872 170 -
Rwork0.352274967187 2596 -
obs--89.8343618058 %
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)
11.73321664303-1.83286423223-1.342754336872.628964912220.1812054811963.58966092324-0.1635705900060.0873327095865-0.1415306663740.0518468620294-0.09725688115-0.109076486440.2702652291110.0428678669679-3.53921241683E-70.727069546946-0.046140013365-0.02662267443610.851613637104-0.01585600550740.809393289857-18.0332614688-81.52081413228.91096904606
21.190748916441.05706789647-0.8853779032661.02184950962-0.00945813210391.5809117128-0.295303898849-0.58189907991-0.3659711681150.4428897998450.165651092458-0.4333388036451.168172778790.667461660721.34804881367E-61.174164128220.179740251528-0.02738414757071.126869214850.07593200026971.0218386065-10.0672722792-83.257963624319.6957385392
33.08618214857-2.231795935740.06722540575894.72089722846-0.4945862646892.19557947728-0.253042034926-0.604218951798-0.05697789529680.7304150738220.2920220464220.02500240036980.2942035405580.2243275340972.40509664847E-80.832050848189-0.004006824990150.03159034508861.00088329846-0.004439782732180.726623323067-19.1229416818-73.764984508624.2486802864
41.57548355661-1.12080420894-0.003705123888094.01734521343-0.78720254352.18671238023-0.124678448841-0.3187776382570.01463516261660.5464323484960.2274448994520.36634900619-0.137523755006-0.05910630539-4.50504766624E-80.704745269741-0.02658482060370.04071350490290.883352267999-0.05055214909030.810546086433-32.8747156191-49.999305588813.993489881
53.63675252461-0.6271928195471.049924957382.614090638650.03038438907222.520542858840.08510568869240.3650770943730.406896014829-0.30272586161-0.111031345882-0.44621904369-0.2681257136530.3401597580125.62564839669E-90.856501840447-0.07527380396530.09111252287820.877914829022-0.01726504292980.919028614901-23.2488946848-43.11951755511.10802913128
63.59133121715-0.657138921457-0.2320110461544.76009245259-0.1898974973743.31868801275-0.0888905659021-0.09660974759130.8971296339120.4162285127440.0345165166218-0.710028595702-0.7400583050410.369705951529-1.22609338044E-70.892896282006-0.0865943969067-0.03224966155060.9114794245-0.0642784462130.946550392036-21.5944623583-40.264512481312.4702621287
70.1822597238380.2614476306310.0358429766280.2217412631240.06026925863080.09240021096670.216452241794-0.9373516218681.16094087612-1.017320564970.2550597345350.401139953871-0.5668645727620.2285944727291.83885869112E-51.330541898930.1194705341410.1336909020331.20035830331-0.1876496948451.73800653092-44.658534819-11.40259488739.1795973218
80.8888759871030.226341005176-0.5449712584910.1699359763450.001991831561870.445514411983-0.08126175434670.132760028183-0.385605291481-0.4984408404760.880853013157-0.209199758083-0.757360165753-0.0499159870866-6.95143571315E-61.720680384480.09174244966840.1101130771690.9331668479910.0737604862391.71889913698-41.8511636581-3.940577032430.605746117049
90.04451303758650.0667365694899-0.06567348340610.125342075827-0.1068086302360.0698111819729-0.603427399627-0.416395979341-0.2219828026111.11049301491-0.2978520838980.871825805472-0.7064740912870.3428611776063.03118508558E-61.529923877240.0101901464950.05427900463091.14170064856-0.1265170763711.14096727815-32.0172063246-18.758165043314.9529449519
100.199480972603-0.108376623676-0.03231676241270.01817902899620.06141832027730.143197331137-0.7164328824540.242383376472-0.00256052376665-0.9994700824990.05466566925511.6154581994-0.249969465409-1.06983693383-1.50418127578E-61.33473000440.0261237119445-0.1268862568011.15115957646-0.1211587389691.8953535955-44.729788845-18.3414372718-1.7759852551
110.3800809048370.0259818687108-0.5884355348280.05192629012640.01057329190620.8058397476030.5739463498410.2180304945050.820207465536-0.0113884786184-0.416932504556-0.8139139932220.757261671097-0.09455860327781.6515216549E-71.26509758965-0.03226745523220.1816799356050.974009837289-0.01421038959561.87199081034-30.3366835055-16.8991505418-0.294470467092
120.06883862054410.00331299474845-0.02011445924090.0375699779943-0.04162695774270.07454659676470.91446007844-0.503562093959-0.5471282908250.113374453254-0.794544926490.8593857433030.140654306847-0.13512271449-2.60243819678E-51.98079725853-0.02612660283370.007618604102370.921976491752-0.06704741002911.42808045763-34.7289838479-11.5051137615-9.72639458138
131.435752850690.378827734715-1.055551035020.5832919950970.02984414432570.7206438067720.3809603763780.09950649460170.5062051972630.330635103842-0.5398476690740.5217516732520.395671169415-0.09689665795835.77111877538E-71.376783137130.03159048638910.04308434813351.12317849768-0.08066386428971.62446510687-36.4588393382-8.390163235071.08332226926
140.5927701140360.600689387207-0.01733691499260.6772408236950.3687200326231.194182908510.1789546738570.331325766951.26676109595-0.0829000597074-0.4237944442530.8565356795620.232690507705-0.01844136344472.74954160199E-61.25865431102-0.01760504262830.06317997134820.931695407086-0.08582145815681.48376219244-36.0323806293-21.59212725231.79134139642
150.08628318436450.1301026935150.03172434843680.1342172144780.006906670715230.04843727686580.192200485985-1.16726318741-0.06514965029310.448404288255-0.198909047587-0.609444444884-1.04414119021-0.3485178675674.26920446813E-61.32264225948-0.05235667352970.170861085771.11251632633-0.07148952402851.64815009888-40.9196357773-23.32705489966.7357896915
160.0376146476317-0.0662421152717-0.01108570919690.04299853907840.08493242138750.155322036206-0.7850526779980.343365721059-0.43621235158-1.32050614869-0.09509361845960.275776797693-0.8933764998460.285903331696-0.008396746896291.1722494160.1664406303330.3598370111710.9824025940730.1207696814761.75449988349-50.0456542974-5.96421766869-3.46163175422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 861 through 912 )
2X-RAY DIFFRACTION2chain 'A' and (resid 913 through 934 )
3X-RAY DIFFRACTION3chain 'A' and (resid 935 through 1089 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1090 through 1149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1150 through 1221 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1222 through 1291 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 11 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 23 )
9X-RAY DIFFRACTION9chain 'B' and (resid 24 through 33 )
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 45 )
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 60 )
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 68 )
13X-RAY DIFFRACTION13chain 'B' and (resid 69 through 91 )
14X-RAY DIFFRACTION14chain 'B' and (resid 92 through 109 )
15X-RAY DIFFRACTION15chain 'B' and (resid 110 through 119 )
16X-RAY DIFFRACTION16chain 'B' and (resid 120 through 126 )

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