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- PDB-7qpu: Botulinum neurotoxin A5 cell binding domain in complex with GM1b ... -

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Basic information

Entry
Database: PDB / ID: 7qpu
TitleBotulinum neurotoxin A5 cell binding domain in complex with GM1b oligosaccharide
ComponentsBotulinum neurotoxin sub-type A5
KeywordsTOXIN / Cell binding domain / receptor / oligosaccharide / neurotoxin
Function / homology
Function and homology information


bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Botulinum neurotoxin sub-type A5
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Toxins / Year: 2022
Title: Crystal Structures of Botulinum Neurotoxin Subtypes A4 and A5 Cell Binding Domains in Complex with Receptor Ganglioside.
Authors: Gregory, K.S. / Mojanaga, O.O. / Liu, S.M. / Acharya, K.R.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin sub-type A5
B: Botulinum neurotoxin sub-type A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1125
Polymers101,4392
Non-polymers6743
Water2,972165
1
A: Botulinum neurotoxin sub-type A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1912
Polymers50,7191
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Botulinum neurotoxin sub-type A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9223
Polymers50,7191
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.165, 129.403, 78.054
Angle α, β, γ (deg.)90.000, 102.961, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Botulinum neurotoxin sub-type A5 / CntA/A5


Mass: 50719.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: cntA, cntA/A5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1IPK2, bontoxilysin
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 150 mM Li2SO4, 50 mM MgCl2 6H2O , 0.1 M HEPES pH 7.8, 4.7% w/v PEG 8K, 4.7% PEG 10K and 4.7% PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→129.4 Å / Num. obs: 33451 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.126 / Net I/σ(I): 4.3
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 22543 / CC1/2: 0.575 / Rpim(I) all: 0.746

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Processing

Software
NameVersionClassification
REFMAC1.19.1_4122refinement
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TWP

6twp


Resolution: 2.4→76.07 Å / SU ML: 0.3514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 1585 4.76 %
Rwork0.2194 31695 -
obs0.2214 33280 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→76.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 44 165 6303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346265
X-RAY DIFFRACTIONf_angle_d0.54598465
X-RAY DIFFRACTIONf_chiral_restr0.0473915
X-RAY DIFFRACTIONf_plane_restr0.00381070
X-RAY DIFFRACTIONf_dihedral_angle_d11.86632317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.33271480.29582885X-RAY DIFFRACTION99.25
2.48-2.570.34661500.29092829X-RAY DIFFRACTION99.1
2.57-2.670.33131190.29132891X-RAY DIFFRACTION99.34
2.67-2.790.30881240.26592914X-RAY DIFFRACTION99.41
2.79-2.940.33711400.25592865X-RAY DIFFRACTION99.67
2.94-3.120.28551300.23772898X-RAY DIFFRACTION99.47
3.12-3.360.28491390.23632884X-RAY DIFFRACTION99.83
3.36-3.70.24391440.19622877X-RAY DIFFRACTION99.87
3.7-4.240.2381380.18652876X-RAY DIFFRACTION99.83
4.24-5.340.22041690.16982876X-RAY DIFFRACTION99.84
5.34-76.070.22021840.21262900X-RAY DIFFRACTION99.64

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