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- PDB-6uc6: Crystal structure of BoNT/B receptor-binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6uc6
TitleCrystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11
Components
  • Botulinum neurotoxin type B
  • JLI-H11
KeywordsHYDROLASE/ANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / receptor-binding domain / TOXIN / ANTITOXIN / HYDROLASE-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 / 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 / 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: 2.32005878384 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
DepositionSep 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
C: JLI-H11
B: Botulinum neurotoxin type B
D: JLI-H11


Theoretical massNumber of molelcules
Total (without water)138,1294
Polymers138,1294
Non-polymers00
Water5,855325
1
A: Botulinum neurotoxin type B
C: JLI-H11


Theoretical massNumber of molelcules
Total (without water)69,0642
Polymers69,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-6 kcal/mol
Surface area24980 Å2
MethodPISA
2
B: Botulinum neurotoxin type B
D: JLI-H11


Theoretical massNumber of molelcules
Total (without water)69,0642
Polymers69,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-7 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.21, 73.276, 76.367
Angle α, β, γ (deg.)87.833, 65.745, 66.551
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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-H11


Mass: 16530.262 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 / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M KCl, 15 % PEG 5000 MME, 0.1 M MES

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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: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.32→44.58 Å / Num. obs: 54491 / % possible obs: 98.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.5066366088 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.9
Reflection shellResolution: 2.32→2.39 Å / Rmerge(I) obs: 0.484 / Num. unique obs: 4465 / CC1/2: 0.81 / Rpim(I) all: 0.484

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NM1

2nm1


Resolution: 2.32005878384→37.4802763841 Å / SU ML: 0.298855072981 / Cross valid method: FREE R-VALUE / σ(F): 1.96873750686 / Phase error: 25.777399118
RfactorNum. reflection% reflection
Rfree0.22226131306 2764 5.07425969782 %
Rwork0.17008565026 51707 -
obs0.172791002619 54471 98.5365412446 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.9821761911 Å2
Refinement stepCycle: LAST / Resolution: 2.32005878384→37.4802763841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8920 0 0 325 9245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008078354917889144
X-RAY DIFFRACTIONf_angle_d1.0181349462712332
X-RAY DIFFRACTIONf_chiral_restr0.04503231497641283
X-RAY DIFFRACTIONf_plane_restr0.003694903876721575
X-RAY DIFFRACTIONf_dihedral_angle_d14.05991767433375
LS refinement shellResolution: 2.3201→2.3601 Å
RfactorNum. reflection% reflection
Rfree0.333830633019 160 -
Rwork0.252666051031 2578 -
obs--97.5071225071 %
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)
12.52522710746-0.5353951016250.3280408995594.111044248160.1007806570251.8471264386-0.0542419803578-0.304734468878-0.1253314950121.25413539806-0.0960036828035-0.6412798205450.3104972039750.1234469843050.1089232182840.795038418498-0.0952166496164-0.1386319930020.3728095004650.03571255210910.39407208297730.1200602748-12.317769754922.603869405
22.51998000664-1.47617630995-0.05893187148443.71237132948-0.4725371304360.7556209797980.04611153094210.1074038884020.2460587690450.422502985569-0.0756365649485-0.233187143793-0.07650578920430.001528421990260.02579169164310.379835538455-0.09997476995630.0294024568930.288466052736-0.01628884650570.227360209118.35539430733.6985760730812.4976468327
31.09237216492-0.0676555889878-0.08857245650452.17777822014-0.8304963252421.362647874810.188033476850.5572770982570.18016951145-0.267187857805-0.1236489137850.3391468932660.0579767839216-0.218338298041-0.1262754908970.336782087039-0.008699979896370.003959349255830.4267301421830.01324815416460.325780163894.953355822418.75088173486-0.222493279957
43.11797863441-0.1966338058910.3008518585515.92034420716-1.409233083123.616222926860.2684608653340.6319592019540.472601740682-0.657307491023-0.0341869426177-0.0048618662427-0.112432674081-0.0460280212522-0.1905242144240.34466950153-0.02141555696410.07533156687080.3960366397520.05244255063660.36465390465415.116994165812.5946730473-0.202597640608
57.760699321560.223429213806-5.749230357851.288262627370.5848156942949.205004037350.2985740528730.1290927471980.8316434637560.3270196377720.1782399935290.731182948333-0.32151833049-0.214858177693-0.589657923520.2622554577760.0318278248809-0.0008733988105550.2895388826540.04849524939440.431469112549-20.213507771810.975682271425.8701450741
65.879251624790.745581203731-4.141560794873.80127177215-0.2460601418152.926576972720.1024075788971.251520730060.152048295587-0.3566400684470.103900904280.408006551355-0.60878447403-1.25035884414-0.2017241820780.27000511330.00267598433658-0.008819560639560.5609404399040.02653958785750.421795126936-15.913593002111.737171677711.6978651561
72.08687873648-0.664595777583-4.389469577290.2216247300371.388999186979.29301576741-0.1903300794670.1424516057920.1597351933430.2260103733570.1093893170190.02432462568160.259390514608-0.06518637686850.1632994330620.314245355134-0.01033078094570.04105660400940.3155937452350.0226395172830.426884755774-10.68228120395.9192622418721.2856179891
82.00183215037-2.14460665693-1.308512224167.321711788613.614579653051.82826738276-0.393912373477-0.2776855015640.3364963860340.5224459736160.786504737878-0.9341945886390.4403997497432.07479290179-0.1016536093910.2086061332750.100678317999-0.05673235519480.688699917011-0.04187513697490.439821390789-8.094400559433.2523929351726.2450903737
96.599947161525.71953725436-5.405589669129.64660756362-7.21703914286.30865657464-0.1487744195710.26442040872-0.887722290519-0.3027450671790.289767833992-0.3992235581481.88821402594-0.291908436694-0.05256382590280.4030418226960.0202240123176-0.03630577106060.2999690272230.01847275534060.597189579086-15.2881229199-3.4944345784717.8537496481
105.048947076972.49863182167-3.505437069946.53779319577-4.659767553769.809301551030.1219187861280.4413229107790.260011446651-0.1681374959640.2082212598740.5648118039720.0650706077566-0.146415528944-0.3887389849350.272207738443-0.07705791512020.02238449027650.4163993272220.04771111953520.447255101151-20.86598655086.5968294721614.8531302557
113.856331357490.556083762176-3.263375876330.494901084012-0.2408181199872.85702106803-0.247078767964-0.139858973785-0.21845068446-0.01344787831110.1893587047930.001389058198310.2368746451980.088431898420.0796883239040.3250095012520.02962663542520.02536767180620.348551483159-0.004033920551170.43670349596-10.39328540174.5226968618922.7755351223
124.43986282488-1.68786631515-3.773756661493.755967852293.167563452054.1651161081-0.762152103467-0.9494650382410.5999908708360.6915256288440.78905630996-0.00509235459916-0.389644169255-0.00185790489993-0.1982220535250.4959956156220.05318414023720.03991500067750.5747010259150.0182900207620.448872759517-5.6976014159615.697321573324.2827293023
135.29337204885.30119646141-4.833080003325.3312783761-4.845996131774.457505267520.5704072899780.2008302885030.5647921118371.106340904680.3594488907480.651246049106-0.355553919293-0.724411448297-0.9377443644710.4464265182610.04709952027420.03277588788050.4138550632990.09080223751810.486620613993-20.74285929377.8829753726835.7915267601
145.346651401021.48740029516-1.38577459713.78675434108-1.223451624824.42077594720.340043752072-0.8217533631640.08632049071510.554987712315-0.319913550423-0.1565942503850.04859018261770.3108328997440.02445349906160.377735707134-0.0444123541987-0.05920424586040.335282125547-0.004778123621240.26958298517211.622105398419.508891831271.2311345167
152.976594136610.994426509637-1.349427761491.84661895155-0.8214935833612.657986451250.03167867051640.048538468171-0.01892965930950.05131989419270.07483599069680.1379449122180.0890034174478-0.205203714392-0.1051467468120.2534895066890.0124909972393-0.02414448866560.246886372881-0.00584465079330.2840310992912.8063369433919.546149779257.9225709401
163.58059764950.767570463296-0.5297886842233.0894887862-0.3005795267353.83946399194-0.01689634087620.5822609910980.0400636409078-0.5680496365140.06296770348570.1168007334480.332085727921-0.269587000295-0.03499451083370.3594170240120.02779074828920.002301512201430.3139911623720.0293302867470.26621931534320.748679939429.175033361737.166968108
172.56920854930.340694414268-0.8965481264642.32004355584-1.103291751633.55734591770.2727148489190.2320856125070.764085709009-0.201671542001-0.0564589057754-0.0398150183183-0.6771216952610.167694009445-0.1118486197090.445029432038-0.01955574845250.05445393365850.2850716339440.06607071664140.48119178556327.234513959244.303204664841.7590766842
183.27862446459-0.0906824792297-1.301650732355.09689949106-0.8549513460574.354427660250.215665612830.4435461587690.844424466464-0.2535288107640.05149793218110.195039946652-0.785979442038-0.18161762522-0.1852689182380.4136049818590.05769037747860.02991540051340.3436092101250.09953492671950.48933495153617.367201340943.57580071639.5115265179
196.11173822889-5.270361769870.07155859587569.67383672791-0.1239508619942.797413367920.2426615284580.1595586486790.735787825668-0.113200922029-0.0471187720039-0.608136842387-0.3077906115810.289255339244-0.2370923561380.308632273846-0.05323905966090.05087964041720.4515945696750.02370383192730.33644234886853.716799876924.665347680236.4380092104
204.10612023138-2.43258246345-0.3603511944517.409795751551.606972974664.689155954480.057971400894-0.2703108021680.02884200152780.158269245684-0.1273834118070.0588339266072-0.001334063688080.08289734366040.06205959643220.194163953631-0.04692090340790.06406496811060.4186362651030.02645416428490.38438509363345.675162678927.66844010245.5257423177
217.15365014749-1.385999249383.413783649012.28539400846-1.643845961534.156615398560.0519103063662-0.469109031590.304286888510.247566571017-0.117179106752-0.078870831901-0.553773499230.7921227614840.05963564403150.358633873121-0.09328514034710.1145733445520.527901917432-0.03428958198490.40811983166154.679811312730.106621424144.5145797825
226.67039096937-4.43054882585-0.6611027207956.521078273041.478139080071.347372611410.090317051870.258989308115-0.0876956623381-0.142957810619-0.0778295494063-0.199721007158-0.006360477682250.170062035859-0.0005245300158740.221693236323-0.0210415031110.04381687817450.3877419837120.07444054312440.33371437711744.147099719422.593244898641.9462702449
235.021409109843.76092635301-2.487174633095.36938171519-1.730023795058.333275340780.3086572573820.307948639962-0.402820928670.0443193343698-0.818638441279-1.035439443241.774416236150.5855263068860.5132554048510.4580061548470.088204048696-0.03676496819590.405550012-0.04924996476590.4032361935356.452896544310.140541722139.1994921143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 862 through 1053 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1054 through 1149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1150 through 1221 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1222 through 1291 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 17 )
6X-RAY DIFFRACTION6chain 'C' and (resid 18 through 32 )
7X-RAY DIFFRACTION7chain 'C' and (resid 33 through 39 )
8X-RAY DIFFRACTION8chain 'C' and (resid 40 through 51 )
9X-RAY DIFFRACTION9chain 'C' and (resid 52 through 67 )
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 83 )
11X-RAY DIFFRACTION11chain 'C' and (resid 84 through 111 )
12X-RAY DIFFRACTION12chain 'C' and (resid 112 through 118 )
13X-RAY DIFFRACTION13chain 'C' and (resid 119 through 127 )
14X-RAY DIFFRACTION14chain 'B' and (resid 862 through 925 )
15X-RAY DIFFRACTION15chain 'B' and (resid 926 through 1089 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1090 through 1149 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1150 through 1221 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1222 through 1291 )
19X-RAY DIFFRACTION19chain 'D' and (resid 0 through 25 )
20X-RAY DIFFRACTION20chain 'D' and (resid 26 through 64 )
21X-RAY DIFFRACTION21chain 'D' and (resid 65 through 83 )
22X-RAY DIFFRACTION22chain 'D' and (resid 84 through 118 )
23X-RAY DIFFRACTION23chain 'D' and (resid 119 through 127 )

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