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- PDB-8r4n: Crystal structure of neutralizing Fab Eq4.Dp46-3A from equine ant... -

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Basic information

Entry
Database: PDB / ID: 8r4n
TitleCrystal structure of neutralizing Fab Eq4.Dp46-3A from equine antivenom bound to short chain three finger alpha-neurotoxin from Dendroaspis polylepis.
Components
  • Eq4.Dp46-3A heavy chain
  • Eq4.Dp46-3A lambda chain
  • 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 speciesEquus caballus (horse)
Dendroaspis polylepis (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWibmer, C.K.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)5R21TW011454-02 United States
Royal SocietyFLR-R1-201782 United Kingdom
CitationJournal: To Be Published
Title: A monoclonal antibody from horses that neutralizes long and short chain three finger neurotoxins
Authors: Wibmer, C.K.
History
DepositionNov 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Eq4.Dp46-3A heavy chain
L: Eq4.Dp46-3A lambda chain
N: Short neurotoxin 1


Theoretical massNumber of molelcules
Total (without water)55,4893
Polymers55,4893
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex purified on S200. Binding of Fab to chain N confirmed by ELISA and in vitro neutralisation assays.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.623, 104.623, 216.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11L-318-

HOH

21L-376-

HOH

31L-382-

HOH

41L-389-

HOH

51L-408-

HOH

61L-409-

HOH

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Components

#1: Protein Eq4.Dp46-3A heavy chain


Mass: 24941.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Antigen specific memory / Source: (gene. exp.) Equus caballus (horse) / Tissue: Blood / Cell: B cell / Gene: IgHV / Plasmid: pcDNA3.4 / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Eq4.Dp46-3A lambda chain


Mass: 22831.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Antigen specific memory / Source: (gene. exp.) Equus caballus (horse) / Tissue: Blood / Cell: B cell / Gene: IgHV / Plasmid: pcDNA3.4 / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Short neurotoxin 1


Mass: 7715.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis polylepis (cobra) / Tissue: Venom / Plasmid: pcDNA3.4 / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01416
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M SPG buffer (pH9.0), 50% PEG1500 / PH range: 8.5-9.5 / Temp details: Wine cabinet

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30760 / % possible obs: 98.73 % / Redundancy: 20 % / Biso Wilson estimate: 47.56 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1052 / Rpim(I) all: 0.01217 / Rrim(I) all: 0.1059 / Net I/σ(I): 30.87
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2869 / CC1/2: 0.89 / CC star: 0.97 / Rpim(I) all: 0.1856 / Rrim(I) all: 1.098 / % possible all: 93.87

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 2836 4.98 %
Rwork0.206 --
obs0.2061 30760 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 0 201 3750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.599
X-RAY DIFFRACTIONf_dihedral_angle_d5.073518
X-RAY DIFFRACTIONf_chiral_restr0.046573
X-RAY DIFFRACTIONf_plane_restr0.004633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.34241280.2762436X-RAY DIFFRACTION88
2.24-2.280.2551380.25242564X-RAY DIFFRACTION92
2.28-2.320.23421350.23742612X-RAY DIFFRACTION94
2.32-2.370.26681430.23132618X-RAY DIFFRACTION95
2.37-2.420.24821400.22942659X-RAY DIFFRACTION97
2.42-2.480.25561430.22132686X-RAY DIFFRACTION96
2.48-2.540.23561410.22342681X-RAY DIFFRACTION97
2.54-2.610.27381390.2482732X-RAY DIFFRACTION98
2.61-2.680.25431430.21812742X-RAY DIFFRACTION98
2.68-2.770.29481400.23312702X-RAY DIFFRACTION98
2.77-2.870.27951470.22262740X-RAY DIFFRACTION99
2.87-2.980.2451460.21742771X-RAY DIFFRACTION99
2.98-3.120.25681480.23322731X-RAY DIFFRACTION99
3.12-3.280.29331480.23052792X-RAY DIFFRACTION100
3.28-3.490.26891380.20652738X-RAY DIFFRACTION100
3.49-3.760.20981400.18552789X-RAY DIFFRACTION100
3.76-4.140.16971490.18672772X-RAY DIFFRACTION100
4.14-4.740.20751400.16572785X-RAY DIFFRACTION100
4.74-5.960.18091420.17342777X-RAY DIFFRACTION100
5.97-500.2221480.21832776X-RAY DIFFRACTION99
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)
12.924-0.5199-1.02982.41570.83843.7541-0.2111-0.5731-0.0160.16250.02610.4924-0.0817-0.4023-0.00050.35240.1150.00710.7236-0.01690.5933-33.386-38.365-39.827
24.3426-1.5618-0.53852.06420.53193.031-0.0607-0.69282.20110.0529-0.05380.1445-0.97890.0987-0.03550.98750.19340.03981.2359-0.10090.8712-17.66-27.231-13.908
33.251-0.87670.49782.24470.3972.4652-0.1555-0.5203-0.28140.23870.19610.12210.13870.04910.00010.33470.05970.03190.42080.06260.338-14.784-47.698-42.451
41.57351.87610.55962.47171.1992.6416-0.2122-1.927-1.19170.77740.1649-0.23791.71580.2644-0.09021.28630.3618-0.07561.76670.12890.5131-9.345-39.235-8.506
51.6044-0.111-1.35090.9720.41541.3878-0.24990.7104-0.869-0.8512-0.04990.29770.4357-0.5662-0.00110.7817-0.1095-0.10350.6677-0.13480.9394-27.446-58.683-66.085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:126 )H1 - 126
2X-RAY DIFFRACTION2( CHAIN H AND RESID 127:211 )H127 - 211
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:113 )L1 - 113
4X-RAY DIFFRACTION4( CHAIN L AND RESID 114:210 )L114 - 210
5X-RAY DIFFRACTION5( CHAIN N AND RESID 1:60 )N1 - 60

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