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- PDB-6ul6: Crystal Structure of BoNT/A-LCHn domain in complex with VNA ciA-D... -

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Basic information

Entry
Database: PDB / ID: 6ul6
TitleCrystal Structure of BoNT/A-LCHn domain in complex with VNA ciA-D12/11/ciA-B5 and VHH ciA-H7
Components
  • BoNT/A
  • ciA-D12/11/ciA-B5
  • ciA-H7
KeywordsTOXIN/ANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / Toxin / Antitoxin / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 ...Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulins / Alpha-Beta Complex / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Bontoxilysin-A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02000221988 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) 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 7, 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 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: BoNT/A
B: ciA-D12/11/ciA-B5
C: ciA-H7


Theoretical massNumber of molelcules
Total (without water)141,9913
Polymers141,9913
Non-polymers00
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-13 kcal/mol
Surface area49760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.288, 90.253, 144.771
Angle α, β, γ (deg.)90.0, 119.037, 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 BoNT/A / BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / ...BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / Neurotoxin type A / Peptidase M27


Mass: 100030.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: a, A, boNT, bont, bonta, ACP52_06670 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Antibody ciA-D12/11/ciA-B5


Mass: 28827.428 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: Antibody ciA-H7


Mass: 13133.512 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 13 % PEG 20000, 0.1 M sodium cacodylate

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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: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.02→47.21 Å / Num. obs: 103999 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.8751899906 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.716 / Num. unique obs: 5169 / CC1/2: 0.648 / Rpim(I) all: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless1.9_1692data scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V0A

3v0a


Resolution: 2.02000221988→47.2074892055 Å / SU ML: 0.186499929088 / Cross valid method: FREE R-VALUE / σ(F): 1.33645969424 / Phase error: 19.9511542728
RfactorNum. reflection% reflection
Rfree0.194475502331 5185 4.98615224834 %
Rwork0.182756746715 98803 -
obs0.183342226535 103988 99.7104228593 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4504074541 Å2
Refinement stepCycle: LAST / Resolution: 2.02000221988→47.2074892055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9562 0 0 799 10361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01555965987499820
X-RAY DIFFRACTIONf_angle_d1.4463788208313313
X-RAY DIFFRACTIONf_chiral_restr0.0735889373121469
X-RAY DIFFRACTIONf_plane_restr0.007917202812271721
X-RAY DIFFRACTIONf_dihedral_angle_d14.07032426353598
LS refinement shellResolution: 2.02000221988→2.043 Å
RfactorNum. reflection% reflection
Rfree0.265695428912 163 -
Rwork0.263679910782 3340 -
obs--99.9714611872 %
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)
11.572693229460.03034717491340.5622106931921.830141518750.4812256010331.471683836710.05674088748810.105294625246-0.137619678457-0.0832453905010.188747203311-0.1176790903160.3886836329080.1429480486360.07386947290110.1998538143560.02432110546340.04604212215930.105678018742-0.01905887799840.0974984861998-31.6608617538-41.419434577519.6273137571
20.8678321593190.3359913294980.337952947751.02484407611-0.001905211408610.8551975742420.0189334154667-0.008434532984940.0593553965490.0672263220470.0404365241196-0.02068440903880.06627799570460.0391395120498-0.002581940151750.1236560349290.01895558268170.04703253054710.144613336847-0.01455043778960.117955914558-32.1031037301-26.276115062826.0838124717
30.286447739746-0.2819208614750.3705000945041.105892148660.3935566031030.924536628558-0.210189647543-0.1141735553970.199241215196-0.02003855008890.001358012983170.370351923063-0.246732404495-0.282618968056-0.01947340982880.2218104356360.03427238856470.04668694401050.334475779938-0.03465732529510.356233708852-35.2788797582-5.8686099827626.6179459458
40.3899696771130.2146168290360.558342170811.052107465080.3466977414860.617372801563-0.06862677656950.092961837681-0.0270915676893-0.1308093234530.0727534666802-0.02061157945610.04260727893150.04201951139640.0005242237452620.218607266867-0.02393634139560.06250832094890.2750860452530.01212985658890.185247492142-25.1250376727-23.289557834724.3201272189
51.688463376180.4502329677780.2674165756830.5989237627130.1812624979750.3882234681230.163117968912-0.04088247777120.244144924110.207546871342-0.165309883418-0.103803565117-0.0600793681377-0.0116503516995-0.01075577469430.269757922914-0.03482043582980.02221011281340.25930021425-0.01368121159680.244196191027-16.2905278775-5.7728925230342.0780800249
60.8568665556620.2759504326780.2887852782350.07471617606710.217447237139-0.166789664601-0.0582944222704-0.4344742210380.1962428470410.353695991348-0.004258447968810.247350514285-0.0276923705601-0.221555695348-0.01140354593970.2775824068390.0322073863010.1174218011950.474562193321-0.07340044210780.475410399847-39.8928369820.93660082014541.2939462583
70.04097561662470.07307658626130.02231837335640.151245864093-0.06367289507060.1699939774780.1868064292960.0463230480125-0.1222818833290.503461114394-0.003189944710940.0118131808086-0.00944844092141-0.0308092477573-4.97934881721E-70.5952674429230.13576156745-0.1191024707930.5641020743310.06409663631130.333651056483-11.399345555-54.036103367258.8374884248
80.624656939471-0.6002621843040.5723728960030.752580420975-0.2594166226461.067971585410.275869615599-0.0527625574304-0.3572314035550.205275146430.01797313176180.2066074882120.6084700907970.1116240480780.0004102098473280.667685143940.12186531006-0.2147616927380.325183794140.03032831241710.323920388081-18.6141844049-55.477655096750.1008303818
90.722384497208-0.332599089151-0.3954186563960.2397294608410.4177852993230.6444264287050.794415979129-0.314392090380.3509069404060.0221974249893-0.0318223199678-0.396637673193-0.2514847300890.2197193381440.05750931041060.70825154139-0.0754449115843-0.06310453936030.5668599837880.07314297611880.575692260908-8.07991982048-39.190467772268.7137627149
101.56334186651-0.0506581404317-0.3039611443170.8174436408580.2894729083870.477612516547-0.185847336073-0.440115984669-0.4256637074920.4551809028580.029025904699-0.1210938399320.505214767446-0.27416636028-0.1429692815620.774402661371-0.443256178896-0.2210903683090.6264726168270.1498731815820.413372344544-7.65413635715-27.708530673268.2937993435
110.1570822648190.1479918358920.1329646923010.1936789746420.2318233575640.565671186738-0.224835361159-0.0008818108409010.0762405557189-0.356739135850.1332325139690.285277105358-0.0754127350818-0.377874097123-0.0570477497440.4773753862480.0472976119455-0.07818669830210.2966209709730.129140542810.333671476377-54.2744564302-10.0501635115-3.35549506857
120.2166700524410.02837247414720.090127841962-0.004092358705350.0007734867300980.0833906792295-0.05533234412190.005942511170260.321427735538-0.3916986389710.2119979968330.0901611815879-0.599194714656-0.183631489115-0.002485096580130.3616253329420.0173599470698-0.03128629695470.2259701036980.06015731134590.351142333476-51.6471246647-5.400425078287.33439143412
130.1254674693680.0267682551869-0.03354749379930.0325482568719-0.03788850497130.0300671633613-0.141993500630.19610391974-0.0154664159391-0.1930785289280.08829026446680.2057362959490.0518369675967-0.270392203784-0.001866980476350.287095489664-0.058408660725-0.1387076516930.205156237160.1257290892070.246412390656-53.5123578135-21.00282537272.29737109038
140.08875438965760.0336710092464-0.0344948528780.0495703298066-0.08821829212810.157611683284-0.1796796011260.140928166770.154640385334-0.3233994274250.1318589265420.107998292889-0.3137085774680.04880535351780.0002270087715680.26687218253-0.0427196769976-0.0198928610240.1714967966250.05510865220680.189958625509-42.6654567305-14.45470196064.5943894259
150.3121993364110.146793457340.1383385096610.330881946122-0.2178187746250.472683527697-0.09811549985050.03057316955910.191848770477-0.4058321531420.0137652488840.325737621201-0.289891687925-0.33597977887-0.01047138224940.341453557356-0.0161255250339-0.0650356081910.1942440010570.08499764320410.242481024079-51.0930544867-12.50828244432.5356882538
160.1439317326630.121425332818-0.05871162787630.105926217082-0.05951791369070.04859383649360.008373271961910.305215792006-0.0368667624804-0.635908853762-0.0288346278257-0.3399934877620.2001827430440.0793347634139-0.01106224760080.4667196655880.00564666601113-0.05700249642240.3737892379090.03039522975980.290796799569-53.5790446472-17.1370148123-10.9036284801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 452 )
3X-RAY DIFFRACTION3chain 'A' and (resid 453 through 495 )
4X-RAY DIFFRACTION4chain 'A' and (resid 496 through 566 )
5X-RAY DIFFRACTION5chain 'A' and (resid 567 through 765 )
6X-RAY DIFFRACTION6chain 'A' and (resid 766 through 866 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 117 )
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 148 )
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 251 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 17 )
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 33 )
13X-RAY DIFFRACTION13chain 'C' and (resid 34 through 45 )
14X-RAY DIFFRACTION14chain 'C' and (resid 46 through 72 )
15X-RAY DIFFRACTION15chain 'C' and (resid 73 through 107 )
16X-RAY DIFFRACTION16chain 'C' and (resid 108 through 114 )

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