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- PDB-9hub: D11 mAbs bound to alpha-Bungarotoxin at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 9hub
TitleD11 mAbs bound to alpha-Bungarotoxin at pH 7.5
Components
  • Alpha-bungarotoxin
  • heavy chain
  • light chain
KeywordsTOXIN / pH / antibody
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsWade, J.W. / Bohn, M.F. / Laustsen, A.H. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20SA0066621 Denmark
CitationJournal: Mabs / Year: 2025
Title: Rational design of antibodies with pH-dependent antigen-binding properties using structural insights from broadly neutralizing antibodies against alpha-neurotoxins.
Authors: Wade, J. / Strancar, N. / Fernandez-Quintero, M.L. / Siebenhaar, S. / Jansen, T. / Meier, E.P.W. / Jenkins, T.P. / Bjorn, S.P. / Nguyen, G.T.T. / Lomonte, B. / Gutierrez, J.M. / Sorensen, C. ...Authors: Wade, J. / Strancar, N. / Fernandez-Quintero, M.L. / Siebenhaar, S. / Jansen, T. / Meier, E.P.W. / Jenkins, T.P. / Bjorn, S.P. / Nguyen, G.T.T. / Lomonte, B. / Gutierrez, J.M. / Sorensen, C.V. / Loeffler, J.R. / Paul, A. / Tulika, T. / Arnsdorf, J. / Schoffelen, S. / Lundquist, E.V.S. / Sorensen, J. / Ward, A.B. / Voldborg, B.G. / Bohn, M.F. / Rivera-de-Torre, E. / Morth, J.P. / Laustsen, A.H.
History
DepositionDec 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: heavy chain
X: Alpha-bungarotoxin
Z: Alpha-bungarotoxin
I: light chain
M: heavy chain
B: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,55013
Polymers77,1166
Non-polymers4347
Water17,312961
1
C: heavy chain
X: Alpha-bungarotoxin
B: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8688
Polymers38,5583
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-8 kcal/mol
Surface area15060 Å2
MethodPISA
2
Z: Alpha-bungarotoxin
I: light chain
M: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6825
Polymers38,5583
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-9 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.051, 84.735, 102.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody heavy chain


Mass: 13187.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia (bacteria)
#2: Protein Alpha-bungarotoxin / Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha- ...Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha-bungarotoxin (A31) / BGTX A31 / Alpha-elapitoxin-Bm2a / Alpha-EPTX-Bm2a / Long neurotoxin 1


Mass: 10297.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60615
#3: Antibody light chain


Mass: 15073.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia (bacteria)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 70% (v/v) MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.33→22.38 Å / Num. obs: 158613 / % possible obs: 99.61 % / Redundancy: 13.3 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1228 / Rpim(I) all: 0.03485 / Net I/σ(I): 8.44
Reflection shellResolution: 1.33→1.34 Å / Rmerge(I) obs: 1 / Num. unique obs: 5216 / CC1/2: 0.341 / Rpim(I) all: 0.341

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→22.38 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 8021 5.08 %
Rwork0.159 149980 -
obs0.1608 158001 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.74 Å2
Refinement stepCycle: LAST / Resolution: 1.33→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 0 28 961 5937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785253
X-RAY DIFFRACTIONf_angle_d0.99627139
X-RAY DIFFRACTIONf_chiral_restr0.0846762
X-RAY DIFFRACTIONf_plane_restr0.0107937
X-RAY DIFFRACTIONf_dihedral_angle_d16.18861913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.340.41322700.42354542X-RAY DIFFRACTION91.6
1.34-1.360.41272690.40214891X-RAY DIFFRACTION98.01
1.36-1.380.40732800.36444931X-RAY DIFFRACTION99.98
1.38-1.390.36822800.34974964X-RAY DIFFRACTION99.98
1.39-1.410.35382800.32854974X-RAY DIFFRACTION100
1.41-1.430.32652800.30244936X-RAY DIFFRACTION99.92
1.43-1.450.31242520.28624961X-RAY DIFFRACTION99.94
1.45-1.470.31482570.26355003X-RAY DIFFRACTION99.98
1.47-1.50.28362540.24454957X-RAY DIFFRACTION99.92
1.5-1.520.27882610.22334993X-RAY DIFFRACTION99.92
1.52-1.550.27592450.21865011X-RAY DIFFRACTION100
1.55-1.580.24342430.20914998X-RAY DIFFRACTION99.96
1.58-1.610.22682410.18795017X-RAY DIFFRACTION99.96
1.61-1.640.21612600.1724974X-RAY DIFFRACTION100
1.64-1.680.22692890.16674955X-RAY DIFFRACTION99.98
1.68-1.710.20613050.15824966X-RAY DIFFRACTION100
1.71-1.760.21792700.14625004X-RAY DIFFRACTION99.96
1.76-1.80.17962760.13645017X-RAY DIFFRACTION99.96
1.8-1.860.17442870.13394936X-RAY DIFFRACTION99.98
1.86-1.920.18752630.13565033X-RAY DIFFRACTION99.98
1.92-1.990.18172520.13225039X-RAY DIFFRACTION100
1.99-2.070.17072470.13345061X-RAY DIFFRACTION100
2.07-2.160.17592830.1364995X-RAY DIFFRACTION99.98
2.16-2.270.16952700.13965055X-RAY DIFFRACTION100
2.27-2.420.16842450.13285052X-RAY DIFFRACTION100
2.42-2.60.1812720.13355043X-RAY DIFFRACTION100
2.6-2.860.15842860.13955076X-RAY DIFFRACTION100
2.86-3.280.17842330.1485143X-RAY DIFFRACTION100
3.28-4.120.18582450.14315177X-RAY DIFFRACTION99.98
4.12-22.380.17453260.15525276X-RAY DIFFRACTION99.4

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