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- PDB-8s72: Crystal structure of neutralizing Fab Eq4.Dp46-3D from equine ant... -

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Basic information

Entry
Database: PDB / ID: 8s72
TitleCrystal structure of neutralizing Fab Eq4.Dp46-3D from equine antivenom bound to a consensus short chain three finger alpha-neurotoxin.
Components
  • Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
  • Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
  • Short neurotoxin 1
KeywordsANTITOXIN / Monoclonal antibody / antivenom / complex / short chain alpha-neurotoxin
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 speciessynthetic construct (others)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsAyres, F. / Wibmer, C.K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust227858/Z/23/Z United Kingdom
Royal Society201782 United Kingdom
CitationJournal: To Be Published
Title: A monoclonal antibody from horses that neutralizes long and short chain three finger neurotoxins
Authors: Ayres, F. / Patel, R. / Casewell, N. / Wibmer, C.K.
History
DepositionFeb 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Short neurotoxin 1
A: Short neurotoxin 1
X: Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
Y: Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
H: Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.
L: Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.


Theoretical massNumber of molelcules
Total (without water)108,9886
Polymers108,9886
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Confirmed by ELISA binding and neutralization assay.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-65 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)294.846, 294.846, 99.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11H-346-

HOH

21L-365-

HOH

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Components

#1: Protein Short neurotoxin 1 / Neurotoxin alpha / Toxin alpha


Mass: 7117.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GPGG linker sequence from tag removal. / Source: (gene. exp.) synthetic construct (others) / Plasmid: pcDNA3.4 / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01426
#2: Antibody Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.


Mass: 24573.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-Terminal GLEVLFQ sequence remnant from HRV3C cleavage.
Source: (gene. exp.) Equus caballus (horse) / Tissue: PBMC / Cell: Memory B cell / Gene: IgHV4 / Organ: Blood / Plasmid: pcDNA3.4 / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.


Mass: 22802.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Tissue: PBMC / Cell: Memory B cell / Gene: IgLV / Organ: Blood / Plasmid: pcDNA3.4 / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris HCl (pH 8,0) 60% MPD Cryoprotected with 10% glycerol
PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 64005 / % possible obs: 99.7 % / Redundancy: 78.5 % / Biso Wilson estimate: 59.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.541 / Rpim(I) all: 0.06 / Rrim(I) all: 0.544 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.78-2.830.929700.3270.458154.94
2.83-2.881.131080.50.3951

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→20.6 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1986 3.13 %
Rwork0.2276 --
obs0.2283 63529 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 0 204 7505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.947
X-RAY DIFFRACTIONf_dihedral_angle_d6.151077
X-RAY DIFFRACTIONf_chiral_restr0.0961191
X-RAY DIFFRACTIONf_plane_restr0.0051310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.850.34241140.32093960X-RAY DIFFRACTION91
2.85-2.930.35991390.31384329X-RAY DIFFRACTION100
2.93-3.010.31481320.29244403X-RAY DIFFRACTION100
3.01-3.110.29041410.27654360X-RAY DIFFRACTION100
3.11-3.220.28081760.26914321X-RAY DIFFRACTION100
3.22-3.350.28481360.24644393X-RAY DIFFRACTION100
3.35-3.50.24781500.22994378X-RAY DIFFRACTION100
3.5-3.680.2741440.21984399X-RAY DIFFRACTION100
3.68-3.910.22221520.20954397X-RAY DIFFRACTION100
3.91-4.210.21551480.19994418X-RAY DIFFRACTION100
4.21-4.630.21571430.184438X-RAY DIFFRACTION100
4.63-5.290.21471410.19434488X-RAY DIFFRACTION100
5.29-6.630.26561380.24154536X-RAY DIFFRACTION100
6.63-20.60.23651320.23264723X-RAY DIFFRACTION100
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)
13.47850.1401-1.18481.37320.75983.0684-0.04720.1032-0.1846-0.110.0798-0.01810.1448-0.20210.00010.53720.0411-0.00760.53110.05440.5215-63.793-62.563-2.621
23.2245-1.45151.74163.5970.26083.360.1296-0.3095-0.42020.749-0.1757-0.55590.28430.17140.00230.69480.046-0.02580.53760.10540.5735-62.964-62.71816.63
33.64991.5877-1.35072.8394-0.74433.2837-0.158-0.1987-0.08720.2903-0.02090.32320.7513-0.09380.00080.9128-0.10920.15770.43910.04320.793-85.515-84.1912.453
41.87921.8912-1.48941.8963-1.38611.87820.08330.360.1616-0.41990.31220.07580.1559-0.3411-0.00141.0934-0.2539-0.04810.6861-0.00721.174-105.271-107.6915.254
52.01370.99060.03532.33750.4472.0001-0.3980.793-0.0209-0.81050.17670.20920.6269-0.1239-0.00040.9817-0.18140.02810.6817-0.02650.7401-83.84-83.24-8.543
61.22850.88560.58862.29871.27411.0592-0.03340.9894-0.106-0.6030.27020.8066-0.3028-0.71140.00041.2423-0.3448-0.14451.05330.27891.4012-114.713-103.49-6.985
72.1674-1.96620.89934.3617-0.90112.6808-0.05060.0394-0.0525-0.2239-0.06350.0428-0.23910.14410.00010.5682-0.0021-0.01380.42860.06270.4362-70.507-32.4222.373
84.42540.00370.36533.7430.93014.70280.0154-0.2760.33670.2630.1384-0.2036-0.12790.2507-00.63140.03220.01330.40720.03370.4078-74.647-1.04411.862
91.4199-0.07580.2782.2251.45754.0507-0.0868-0.282-0.05540.22630.0330.0451-0.2432-0.0410.00010.55550.0392-0.00610.50570.0690.4729-68.635-34.68923.209
104.95-2.44660.72074.70040.14483.9641-0.0437-0.0581-0.15820.1999-0.03020.3240.3607-0.1347-0.00050.737-0.0990.03980.3805-0.00550.4615-85.109-0.73323.275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN N AND RESID -3:60 )N-3 - 60
2X-RAY DIFFRACTION2( CHAIN A AND RESID -3:60 )A-3 - 60
3X-RAY DIFFRACTION3( CHAIN X AND RESID 2:123 )X2 - 123
4X-RAY DIFFRACTION4( CHAIN X AND RESID 124:213 )X124 - 213
5X-RAY DIFFRACTION5( CHAIN Y AND RESID 2:112 )Y2 - 112
6X-RAY DIFFRACTION6( CHAIN Y AND RESID 113:208 )Y113 - 208
7X-RAY DIFFRACTION7( CHAIN H AND RESID 2:123 )H2 - 123
8X-RAY DIFFRACTION8( CHAIN H AND RESID 124:216 )H124 - 216
9X-RAY DIFFRACTION9( CHAIN L AND RESID 2:112 )L2 - 112
10X-RAY DIFFRACTION10( CHAIN L AND RESID 113:211 )L113 - 211

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