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

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Basic information

Entry
Database: PDB / ID: 6uft
TitleCrystal structure of BoNT/B receptor-binding domain in complex with VHH JLK-G12
Components
  • Botulinum neurotoxin type B
  • JLK-G12
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 / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-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: 2.90008139771 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 25, 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: JLK-G12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7344
Polymers69,5422
Non-polymers1922
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-36 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.24, 53.1899, 114.41
Angle α, β, γ (deg.)90.0, 92.35, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 52534.145 Da / Num. of mol.: 1
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 JLK-G12


Mass: 17007.889 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)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 14 % PEG 8000, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→38.28 Å / Num. obs: 20044 / % possible obs: 96.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 53.409365795 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.12 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.611 / Num. unique obs: 3260 / CC1/2: 0.684 / Rpim(I) all: 0.61

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Processing

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

2nm1


Resolution: 2.90008139771→38.2777810241 Å / SU ML: 0.487272570681 / Cross valid method: FREE R-VALUE / σ(F): 1.35003060314 / Phase error: 28.2555588931
RfactorNum. reflection% reflection
Rfree0.257539668402 1029 5.13832018376 %
Rwork0.212482169622 --
obs0.214808450038 20026 96.2048424289 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.2824239641 Å2
Refinement stepCycle: LAST / Resolution: 2.90008139771→38.2777810241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 10 14 4603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003963261969934714
X-RAY DIFFRACTIONf_angle_d0.6966679638646357
X-RAY DIFFRACTIONf_chiral_restr0.0292863390444654
X-RAY DIFFRACTIONf_plane_restr0.00277876611449815
X-RAY DIFFRACTIONf_dihedral_angle_d13.19415374351744
LS refinement shellResolution: 2.9001→3.0529 Å
RfactorNum. reflection% reflection
Rfree0.398134087388 144 -
Rwork0.320872513096 2727 -
obs--97.5866757308 %
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)
11.711835062341.38651394795-0.1365280857470.6023735710950.7898956938711.410358591460.125305426788-0.0576785928164-0.04251286457740.0859811760657-0.110275831462-0.0687350468883-0.06692932181750.2721140677122.07188351794E-80.438717019823-0.0291123410989-0.0272085821120.3605899659750.03931020183020.35342238474533.96228058510.402867492572131.298972074
20.253004813449-0.0136768388105-0.05796323438890.398040976313-0.6578861356640.2432937235990.00803695484701-0.7328767694480.9501429675290.536592533136-0.4266887485020.504913867867-0.330574170273-0.1410476683731.35180456154E-70.538250525395-0.1108955989070.1164507764690.631758803947-0.09792513083230.6733884101326.00316966318.76232747955138.797656159
32.69070051729-0.478145158772-0.00282014522330.772949592227-0.5741289930921.91922504173-0.0483991492777-0.5442731275310.2727213329350.324612793227-0.4460987573430.3899875321810.131880567029-0.634150597626-1.04628252926E-80.414577451744-0.1514734370550.1380497707090.551707047596-0.1092718569310.4726620687513.8692645929-2.55901397243134.600044969
41.038096602270.2797215076920.6174362647050.193093551237-0.2268034631821.462556947170.0561540412737-0.6746512161130.3605407411680.553176873-0.2199013454060.4378989958430.283720111179-0.410694924564-3.26623422487E-80.589742722241-0.1430650268730.08413953259050.805410350351-0.2049082701850.50543555267320.2707759617-1.86999797819141.65350137
51.001782055180.1463562452210.5803165759990.8069556903331.035979902364.97987272322-0.139973340816-0.02685827080990.255662111169-0.108897568585-0.08028286468710.108556346583-0.0717434087837-0.0502183588913-9.95167127179E-110.2438816038940.0162630481162-0.008064053751940.2261358280630.01419892417910.43795748104717.1645569128-4.4008824135105.840773244
62.219500323060.2868211851030.4502962196621.30694903171.226856278012.44648379091-0.1491136778740.3370757952310.554168702016-0.316758409615-0.1686322361640.147189965432-0.521989693973-0.278256923617-4.47233807021E-110.4067274148190.0381374764887-0.05345694951730.3612983482260.01810032705540.4575508400188.71108936592-1.4669739634498.5506188985
70.273684405011-0.1585672341170.1473678567510.322902870020.1099105291490.00654564107592-0.5276402143630.00386070454766-0.2592422809760.156937965581-0.1560094733480.07564858962920.8150890054540.09186226284291.53628582587E-70.702272006358-0.00206453950824-0.1011596403220.6351886852320.000292166039540.526128267218-1.61679285409-22.533709391566.8569687062
80.0148016435917-0.00409437975399-0.0529342363153-0.05646222765550.0695399570805-0.00512727012708-0.45473111047-0.2810509220181.459391769330.0268229063123-0.446518756950.34752320634-0.312574928567-0.1773497661775.17816066998E-60.61254523172-0.0851158359531-0.09405311112930.67979924215-0.007944465823370.541100022816-4.00332838664-17.06960848568.8796835324
90.05411569239580.0122077506562-0.04985965666180.01464361519120.03740148464750.03822472101420.0930529849881-0.001093779816890.467118666017-0.01107617191970.01723352879371.342982856760.0617762543759-0.8386869136981.03692966245E-50.5248898551640.129878421707-0.0182830277890.539250532941-0.0380372754870.64443835899-4.47712929612-10.830994553882.008804705
100.07128003717810.07980090006320.1253341905290.09228719887860.1857012832730.0798728536990.4268929049240.1266401851040.02582029487660.07908537894010.0939657277555-1.281371999490.7376227879540.3509786771871.59076508243E-60.804069309817-0.0283417613598-0.1784393890460.5199424976620.005766873521830.583957743069.03902029431-23.368064477571.8833399288
110.2199223909630.281884727755-0.08758005090520.0638719763935-0.103553052910.175736134453-0.5701797488350.7275315815560.0893470717999-0.3461125827390.0710382919106-0.310211007734-0.633738633936-0.3458812156568.36902769424E-80.6820960763780.0120077499852-0.06696989197990.7540038181130.01595566967120.4427845799916.86441016923-8.7327523456271.6809205055
120.01424045168170.0249985346106-0.05996832506010.298674331426-0.2507152355940.13592472246-0.7227907310770.2678750723130.5221407767150.08395728316810.682023379693-0.169884471205-0.4190706573460.5460260060456.62840751266E-70.667103192357-0.072926347969-0.005434789729560.7046149956490.01113075742030.3951526703096.76198896286-11.214739053965.0935514047
130.2652287885570.6241084427280.1953791360520.721773653304-0.4712616005810.462347040096-0.2494420672150.113226754855-0.267636699168-0.424779487858-0.1346822648510.350439432492-0.101200471636-0.24047053059-2.68730984151E-70.5536213383920.0834743414834-0.03726938464880.6875672459690.1290313319650.5754129961581.39414302737-15.359635723664.5069323556
140.02493423340990.0248363964373-0.0176696680223-0.0111401250342-0.04806478441430.046393374973-0.299099105987-0.229795569394-0.457716734034-0.4522871440720.08992645833430.8763220129180.395275187626-0.237244360195-3.90141252111E-60.6051048949320.0124618520163-0.1792404066420.6377898158610.005962291995390.3418631612553.66440596832-22.401364083171.8698624132
150.004766135191680.09242312659140.000220261549868-0.109088727256-0.08428878712080.00491578295733-0.1299842821310.2592521411160.00757670613095-0.0468427892732-0.422243732621-0.225035622611-0.7805704909430.4279386181954.24591960747E-70.3578328607450.0537742953334-0.1014577139140.5595446214780.04900634759140.40805641932310.0496671313-10.857980489879.5824029853
160.0585629153099-0.0337554401338-0.09963042852970.0729314077316-0.04967930577170.101915236354-0.00918857814321-0.0422868618498-0.247802003722-0.463963786848-0.1790310786930.3932184691630.713603627098-0.1983398274364.7126101995E-70.525444004789-0.0574539779872-0.0443690468010.3864282964150.001140907210550.5249421984154.42675521898-19.637246878680.4970874108
170.04342990499740.0583436626181-0.005001032230060.1108420297990.02986598959710.0138074598052-0.1332841315860.627709324771-0.3551667047250.1068380494890.439830583790.1280049024950.184759580565-0.0752128321916-1.35400216027E-61.00057415904-0.0692314024281-0.006387468442780.5118851445370.04170985622020.7046442455793.9771985453-27.894377203658.252040221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 862 through 912 )
2X-RAY DIFFRACTION2chain 'A' and (resid 913 through 934 )
3X-RAY DIFFRACTION3chain 'A' and (resid 935 through 1024 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1025 through 1053 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1054 through 1221 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1222 through 1291 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 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 73 )
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 91 )
14X-RAY DIFFRACTION14chain 'B' and (resid 92 through 98 )
15X-RAY DIFFRACTION15chain 'B' and (resid 99 through 109 )
16X-RAY DIFFRACTION16chain 'B' and (resid 110 through 119 )
17X-RAY DIFFRACTION17chain 'B' and (resid 120 through 128 )

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