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- PDB-7uia: Crystal structure of BoNT/E receptor binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7uia
TitleCrystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH
Components
  • Neurotoxin type E
  • SV2Ac
  • VHH-G6
KeywordsTOXIN / toxin-receptor complex
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Neurotoxin type E
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
Clostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLiu, Z. / Jin, R. / Chen, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2.
Authors: Liu, Z. / Lee, P.G. / Krez, N. / Lam, K.H. / Liu, H. / Przykopanski, A. / Chen, P. / Yao, G. / Zhang, S. / Tremblay, J.M. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Dong, M. / Jin, R.
History
DepositionMar 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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
B: VHH-G6
C: SV2Ac
E: VHH-G6
F: SV2Ac
D: Neurotoxin type E
A: Neurotoxin type E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,91922
Polymers147,9656
Non-polymers2,95516
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.742, 172.335, 137.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 4 molecules CFDA

#2: Protein SV2Ac


Mass: 12198.499 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
#3: Protein Neurotoxin type E


Mass: 47392.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A5H0J8

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Antibody , 1 types, 2 molecules BE

#1: Antibody VHH-G6


Mass: 14390.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca)
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)

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Sugars , 2 types, 8 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 167 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 0.2 M potassium sulfate, 20% PEG 3350, and 5% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.59→137.16 Å / Num. obs: 52103 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 19.9
Reflection shellResolution: 2.59→2.67 Å / Num. unique obs: 4444 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFZ, 5JLV, 6GLW

3ffz

5jlv

6glw


Resolution: 2.59→109.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.9 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24897 2660 5.1 %RANDOM
Rwork0.22595 ---
obs0.22711 49418 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.741 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å20 Å20 Å2
2---2.89 Å20 Å2
3----2.06 Å2
Refinement stepCycle: 1 / Resolution: 2.59→109.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10169 0 182 160 10511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01310585
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179134
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.65814379
X-RAY DIFFRACTIONr_angle_other_deg1.2541.59521219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18851252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52123.919592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.164151710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921542
X-RAY DIFFRACTIONr_chiral_restr0.0410.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.255.6935026
X-RAY DIFFRACTIONr_mcbond_other2.255.6925025
X-RAY DIFFRACTIONr_mcangle_it3.6178.5336272
X-RAY DIFFRACTIONr_mcangle_other3.6178.5336273
X-RAY DIFFRACTIONr_scbond_it2.0445.7575559
X-RAY DIFFRACTIONr_scbond_other2.0325.7475532
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.38.588066
X-RAY DIFFRACTIONr_long_range_B_refined5.17562.61111326
X-RAY DIFFRACTIONr_long_range_B_other5.15362.60411316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 195 -
Rwork0.403 3597 -
obs--99.61 %

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