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- PDB-5l21: Crystal structure of BoNT/A receptor binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5l21
TitleCrystal structure of BoNT/A receptor binding domain in complex with VHH C2
Components
  • Botulinum neurotoxin type A
  • VHH-C2
KeywordsTOXIN / Neutralizing antibody / VHH / Botulinum neurotoxin / BoNT-A-VHH complex
Function / homology
Function and homology information


host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsYao, G. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI125704-01 United States
CitationJournal: Sci Rep / Year: 2017
Title: A camelid single-domain antibody neutralizes botulinum neurotoxin A by blocking host receptor binding.
Authors: Yao, G. / Lam, K.H. / Weisemann, J. / Peng, L. / Krez, N. / Perry, K. / Shoemaker, C.B. / Dong, M. / Rummel, A. / Jin, R.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 A
B: VHH-C2


Theoretical massNumber of molelcules
Total (without water)63,2042
Polymers63,2042
Non-polymers00
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-9 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 103.720, 64.700
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 49877.488 Da / Num. of mol.: 1 / Mutation: T1158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A) (bacteria)
Strain: Hall / ATCC 3502 / NCTC 13319 / Type A / Gene: botA, CBO0806, CLC_0862 / Production host: Escherichia coli (E. coli)
References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Antibody VHH-C2


Mass: 13326.828 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% polyethylene glycol 6,000; 100 mM Sodium Acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.68→35.99 Å / Num. obs: 74608 / % possible obs: 99.5 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.8
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.843 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FUO

3fuo


Resolution: 1.68→35.99 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.11
RfactorNum. reflection% reflection
Rfree0.205 3773 5.06 %
Rwork0.1925 --
obs0.1931 74540 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 0 566 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054550
X-RAY DIFFRACTIONf_angle_d0.9616149
X-RAY DIFFRACTIONf_dihedral_angle_d12.7381690
X-RAY DIFFRACTIONf_chiral_restr0.073653
X-RAY DIFFRACTIONf_plane_restr0.003796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70130.26931270.27452657X-RAY DIFFRACTION100
1.7013-1.72370.22211400.27032657X-RAY DIFFRACTION100
1.7237-1.74730.2511480.25882561X-RAY DIFFRACTION100
1.7473-1.77220.25011520.2592599X-RAY DIFFRACTION100
1.7722-1.79870.2521480.2432657X-RAY DIFFRACTION100
1.7987-1.82680.26411400.23292579X-RAY DIFFRACTION100
1.8268-1.85670.24041390.24092653X-RAY DIFFRACTION100
1.8567-1.88870.22481550.23232597X-RAY DIFFRACTION100
1.8887-1.92310.23141340.22942636X-RAY DIFFRACTION99
1.9231-1.96010.24241340.22722596X-RAY DIFFRACTION100
1.9601-2.00010.22551250.22022657X-RAY DIFFRACTION100
2.0001-2.04360.23321350.212591X-RAY DIFFRACTION100
2.0436-2.09110.24361400.21312689X-RAY DIFFRACTION100
2.0911-2.14340.20611460.20652572X-RAY DIFFRACTION100
2.1434-2.20130.21741550.20862625X-RAY DIFFRACTION100
2.2013-2.26610.21651190.19982667X-RAY DIFFRACTION100
2.2661-2.33920.18251360.20152614X-RAY DIFFRACTION100
2.3392-2.42280.22381330.20222628X-RAY DIFFRACTION100
2.4228-2.51980.22331480.19812623X-RAY DIFFRACTION100
2.5198-2.63450.23171630.19792617X-RAY DIFFRACTION100
2.6345-2.77330.19041510.1962599X-RAY DIFFRACTION99
2.7733-2.9470.19711320.19452660X-RAY DIFFRACTION99
2.947-3.17440.21171340.18232593X-RAY DIFFRACTION99
3.1744-3.49360.1761290.17072623X-RAY DIFFRACTION99
3.4936-3.99860.17531410.16252598X-RAY DIFFRACTION98
3.9986-5.03560.17731180.1522658X-RAY DIFFRACTION99
5.0356-360.19081510.18172561X-RAY DIFFRACTION96
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)
10.35920.15610.07561.2288-0.30330.1347-0.01160.0293-0.0894-0.24120.05680.07720.0496-0.04860.00540.113-0.018-0.00720.13280.00810.143314.18940.1397-5.2158
20.14730.0478-0.05610.1072-0.09510.12210.2042-0.20130.12090.6508-0.1187-0.0169-0.3281-0.00650.08060.6657-0.1058-0.06010.27070.0223-0.01319.30112.978225.794
32.8990.425-2.72591.6988-1.8093.77620.4217-0.81250.19650.5808-0.2663-0.1505-0.3260.5457-0.16030.4452-0.1227-0.21630.4633-0.1170.840544.176822.042614.0085
42.017-0.04730.26990.07170.17350.4850.08940.0250.1883-0.01880.0014-0.2068-0.0510.08440.00510.0689-0.01390.01380.33990.04020.938950.702321.3539-0.7136
54.9068-2.42592.43271.2136-0.87398.76790.1219-0.3368-0.29470.4785-0.0538-0.15050.1626-0.2176-0.08330.7237-0.2309-0.34880.55360.23270.646738.363311.991220.1955
61.6285-1.03820.14232.6702-0.12910.55820.0263-0.1346-0.29250.1494-0.0491-0.6705-0.02530.0490.03540.09070.0039-0.03490.17620.01950.46936.250416.94370.5348
71.43380.1384-0.56320.54860.21791.12570.1005-0.1628-0.37420.08850.0687-0.51070.0750.1435-0.10260.13050.0321-0.01180.2590.05660.821645.303712.897-0.1982
83.26051.3868-2.86762.7722-1.56932.58610.1489-0.09710.09570.1646-0.1518-0.698-0.08060.2236-0.04050.1339-0.0159-0.05590.21150.0390.596841.48922.3222-0.2657
96.134-0.5542-0.04536.22341.14063.22020.0450.66520.3557-0.7250.1211-1.2865-0.33540.506-0.14470.2666-0.06060.1170.35830.04940.888849.010429.3312-8.2349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 869 through 1101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1102 through 1296 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 32 )
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 67 )
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 111 )
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 119 )

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