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

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Basic information

Entry
Database: PDB / ID: 6uht
TitleCrystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10
Components
  • Botulinum neurotoxin type B
  • JLI-G10
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: 2.20001465977 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.P. / Mcnutt, P.M. / Shoemaker, C.B. / Jin, R.
History
DepositionSep 28, 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 / struct_ncs_dom_lim
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
Revision 1.2Oct 30, 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: Botulinum neurotoxin type B
C: JLI-G10
D: JLI-G10


Theoretical massNumber of molelcules
Total (without water)135,1514
Polymers135,1514
Non-polymers00
Water7,350408
1
A: Botulinum neurotoxin type B
C: JLI-G10


Theoretical massNumber of molelcules
Total (without water)67,5762
Polymers67,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-6 kcal/mol
Surface area24720 Å2
MethodPISA
2
B: Botulinum neurotoxin type B
D: JLI-G10


Theoretical massNumber of molelcules
Total (without water)67,5762
Polymers67,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-6 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.147, 223.147, 58.491
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNILEILEchain 'A'AA862 - 9179 - 64
121VALVALSERSERchain 'A'AA922 - 115169 - 298
131ASNASNLEULEUchain 'A'AA1157 - 1274304 - 421
141LEULEUGLUGLUchain 'A'AA1276 - 1291423 - 438
211ASNASNILEILEchain 'B'BB862 - 9179 - 64
221VALVALSERSERchain 'B'BB922 - 115169 - 298
231ASNASNLEULEUchain 'B'BB1157 - 1274304 - 421
241LEULEUGLUGLUchain 'B'BB1276 - 1291423 - 438
112VALVALTYRTYRchain 'C'CC5 - 10710 - 112
122PROPROSERSERchain 'C'CC109 - 126114 - 131
212VALVALVALVALchain 'D'DD27
222GLUGLUTYRTYRchain 'D'DD6 - 10711 - 112
232PROPROSERSERchain 'D'DD109 - 126114 - 131

NCS ensembles :
ID
1
2

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Components

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


Mass: 52534.145 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
#2: Antibody JLI-G10


Mass: 15041.563 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 20000 and 0.1 M MES pH 6.5

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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: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→111.57 Å / Num. obs: 84263 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.7319682932 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.076 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.722 / Num. unique obs: 4520 / CC1/2: 0.733 / Rpim(I) all: 0.565

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Processing

Software
NameVersionClassification
PHASER1.9_1692phasing
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NM1

2nm1


Resolution: 2.20001465977→96.6254853891 Å / SU ML: 0.24787632525 / Cross valid method: FREE R-VALUE / σ(F): 1.33786967781 / Phase error: 23.1584434815
RfactorNum. reflection% reflection
Rfree0.211016532578 4213 5.00142456907 %
Rwork0.194221152895 --
obs0.195082532664 84236 99.0440804713 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.2212800912 Å2
Refinement stepCycle: LAST / Resolution: 2.20001465977→96.6254853891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9143 0 0 408 9551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008190097599859372
X-RAY DIFFRACTIONf_angle_d1.1201163015912659
X-RAY DIFFRACTIONf_chiral_restr0.05371427647451319
X-RAY DIFFRACTIONf_plane_restr0.005690503694521617
X-RAY DIFFRACTIONf_dihedral_angle_d12.6986305763462
LS refinement shellResolution: 2.20001465977→2.225 Å
RfactorNum. reflection% reflection
Rfree0.328672408362 134 -
Rwork0.283037318267 2670 -
obs--99.7864768683 %
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)
10.398730865350.369358616642-0.1436641078130.303548288794-0.1256147864670.18385359441-0.0721813896886-0.01912291292840.00945740514040.156345614485-0.0494048076220.0521587282034-0.0190212716589-0.00670819943294-2.33168171433E-80.2448728310890.03112801265250.003312383181360.210297894889-0.02394544735640.208544486612-128.4329314258.9303832618711.9863881046
20.601962751074-0.150872077843-0.4309684250.3276052957240.0476275343280.4103710964930.04960911324270.08353479897610.1504851044860.0590315011588-0.0531118416778-0.0376703033156-0.128702365393-0.0152291447683-3.4177103193E-50.2415310136820.0451546490903-0.01283396884030.1523210154110.02226500012380.178559753293-121.04467298922.48168211587.58023134386
30.626716727709-0.19026926994-0.1577889733240.135337513635-0.07163684733280.3967661629530.0144939936201-0.00950728201129-0.04187258406710.0182904222591-0.0406511255432-0.003479002448310.002957916878710.0367088574488-4.1586145186E-90.1727605579360.00269664182492-0.008828111593760.1194456507710.03894963433410.155075798348-91.96672970549.46336309099-1.82237208802
40.3580898784460.374322580747-0.2691960723310.1537715058550.2671090074390.2380405112080.0935337027486-0.10707405542-0.1192255537250.0388872665513-0.067833620703-0.09680771076150.02891359053640.101430081495-3.93084924597E-80.218965109503-0.0173441667203-0.01993754293210.1675037704910.0512750576520.187055886363-87.587909806115.45308526784.9841225617
50.398696554348-0.1106584144740.09310826880350.4871913008770.1099636407670.078632061597-0.1457770380.0647974258183-0.01161931414450.19724552450.171067111321-0.04799090907380.1022082295820.03144325932490.001264960040630.3853709120240.0344796250106-0.05099058035640.3027832909690.06317828210850.221828675462-65.1288675612-32.42013818797.46527139323
60.329427411605-0.348885006779-0.1217886208510.54141555711-0.2337439750060.294292032943-0.1017609957190.1532209254740.1491574708240.1278497643340.08810318617770.0216365939830.0284423340833-0.0667417258381-1.09938033699E-90.315764650041-0.0205070417538-0.05048051738580.3348880662390.07680937548790.219232356158-71.6849188584-25.11089113632.59080504392
70.313880740770.103830388799-0.3996421049980.243523739560.05772352827850.2171691326730.0730947990516-0.02691066329610.09518297158050.01654561903290.00190197361186-0.554738778610.07993376078710.08713546556470.09354152711960.3078263188120.0378626543546-0.03018452475280.4529986918460.135375679110.598935655679-43.1518742035-15.8738760298-9.14179560125
80.071352722507-0.1760300330960.05526142594270.358296825493-0.1100298133040.4166230474120.08807231083090.04862532321820.1488597036350.0928646573834-0.13827809374-0.546816548626-0.05728727936850.0957212404113-9.93881557395E-100.249485896617-0.0405421113853-0.05171493071090.3735253142850.1199664890110.622037160561-43.3182763312-3.29045292545-5.8383209516
9-0.0002064730965560.04069848878150.03972150118430.03363053162140.03973932880210.0803392596022-0.0958211424064-0.02403096963180.156484160576-0.097875714529-0.0252996781484-0.143119514207-0.11019505698-0.0258337800922-0.01018352342970.332106383022-0.0830743455785-0.04949335284550.2797933747870.0539009667410.374784885734-77.955338604450.089028801911.0162060589
100.0459627610916-0.0247189981453-0.02659317963730.2993060153970.2010247730240.15795877676-0.0631318169705-0.0724418545304-0.0101624073721-0.01056098782730.005222881373260.126468697704-0.0456422324173-0.0639149256196-1.14961991265E-70.282215422248-0.05056808231830.005961946312150.238111492310.0195080465650.263562482184-83.685685097435.68243889158.33709396366
110.0127542738951-0.02460074979560.03167728928960.02095732233630.0223069001290.0178379101822-0.0760624531471-0.0450776481650.03078885177870.04969701159230.0138753794110.1001933063520.175816283279-0.11978119634-6.36285365943E-70.330034324803-0.07150656307040.01838467808730.3308744888220.03689895266040.297095369814-77.418350871240.375666192515.3006418601
120.0480660789930.0165601329320.03752092317230.1130969649750.2288000752810.1000154410250.0267129722180.002076918965870.00271133939673-0.184974831746-0.1687090312670.141490151893-0.08812729497940.0866145584624-0.01245894601680.319741757922-0.0586517001032-0.04544082193180.2452786011020.05725684915270.312261286496-82.164875213940.78229430274.37582347256
130.1192497163980.00901579210251-0.1035052798340.2739356008140.04358246509490.0279200924821-0.00140954524774-0.00317303476136-0.133965026315-0.19066452087-0.0477803083802-0.1251362180690.032664055806-0.05252881550852.87089581615E-80.29399981526-0.00398371780450.05499094877040.2987375214450.09239384436240.317542391559-63.150020013810.2335980252-18.1744171253
140.02154483648990.03031145428230.02451216675470.07349582890290.05234739418040.00581467396303-0.162798191333-0.07977449916790.1124892856970.119491839954-0.0523358315835-0.128044004113-0.04771486392740.05797364938584.0744829312E-70.315267093336-0.0105313048050.05475067179360.3225210571140.05431557248010.343276264979-62.362109047618.6593311538-16.1381138742
15-0.0106187709031-0.0725606376126-0.04218700030150.09988296064210.03499820218570.04282784801920.007893697460270.0183073921882-0.167783261125-0.128476093870.0631754261711-0.116822727062-0.136052942836-0.0278688610453-3.88596271032E-70.383597723867-0.02076326921040.0550132782680.3815051198490.08253943262980.383531507795-61.27004896479.31416252924-23.2097225496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 856 through 925 )
2X-RAY DIFFRACTION2chain 'A' and (resid 926 through 1089 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1090 through 1221 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1222 through 1291 )
5X-RAY DIFFRACTION5chain 'B' and (resid 862 through 947 )
6X-RAY DIFFRACTION6chain 'B' and (resid 948 through 1089 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1090 through 1181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1182 through 1291 )
9X-RAY DIFFRACTION9chain 'C' and (resid 5 through 23 )
10X-RAY DIFFRACTION10chain 'C' and (resid 24 through 66 )
11X-RAY DIFFRACTION11chain 'C' and (resid 67 through 86 )
12X-RAY DIFFRACTION12chain 'C' and (resid 87 through 128 )
13X-RAY DIFFRACTION13chain 'D' and (resid -3 through 66 )
14X-RAY DIFFRACTION14chain 'D' and (resid 67 through 85 )
15X-RAY DIFFRACTION15chain 'D' and (resid 86 through 126 )

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