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- PDB-8v13: Crystal structure of Black mamba toxin in complex with Centi-SNX-... -

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Basic information

Entry
Database: PDB / ID: 8v13
TitleCrystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody
Components
  • Centi-SNX-B03 Fab heavy chain
  • Centi-SNX-B03 Fab light chain
  • Short neurotoxin 1
KeywordsANTITOXIN/IMMUNE SYSTEM / antivenom / 3-finger toxin / short neurotoxin / antibody / ANTITOXIN-IMMUNE SYSTEM complex
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)
Dendraspis polylepis polylepis (black mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPletnev, S. / Glanville, J. / Kwong, P.D.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2025
Title: Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies.
Authors: Glanville, J. / Bellin, M. / Pletnev, S. / Zhang, B. / Andrade, J.C. / Kim, S. / Tsao, D. / Verardi, R. / Bedi, R. / Liao, S. / Newland, R. / Bayless, N.L. / Youssef, S. / Tully, E.S. / ...Authors: Glanville, J. / Bellin, M. / Pletnev, S. / Zhang, B. / Andrade, J.C. / Kim, S. / Tsao, D. / Verardi, R. / Bedi, R. / Liao, S. / Newland, R. / Bayless, N.L. / Youssef, S. / Tully, E.S. / Bylund, T. / Kim, S. / Hirou, H. / Liu, T. / Kwong, P.D.
History
DepositionNov 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Centi-SNX-B03 Fab heavy chain
L: Centi-SNX-B03 Fab light chain
T: Short neurotoxin 1
h: Centi-SNX-B03 Fab heavy chain
l: Centi-SNX-B03 Fab light chain
t: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8308
Polymers107,7846
Non-polymers462
Water15,493860
1
H: Centi-SNX-B03 Fab heavy chain
L: Centi-SNX-B03 Fab light chain
T: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9154
Polymers53,8923
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-38 kcal/mol
Surface area23040 Å2
MethodPISA
2
h: Centi-SNX-B03 Fab heavy chain
l: Centi-SNX-B03 Fab light chain
t: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9154
Polymers53,8923
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-37 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.539, 72.252, 179.656
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Centi-SNX-B03 Fab heavy chain


Mass: 24222.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Centi-SNX-B03 Fab light chain


Mass: 22741.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Short neurotoxin 1 / Neurotoxin alpha


Mass: 6928.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendraspis polylepis polylepis (black mamba)
Production host: Dendroaspis polylepis polylepis (black mamba)
References: UniProt: P01416
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 20% PEG4000, 0.2M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979497 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979497 Å / Relative weight: 1
ReflectionResolution: 1.8→30.01 Å / Num. obs: 121160 / % possible obs: 98.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Rrim(I) all: 0.056 / Χ2: 0.9 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.863.80.809119100.7110.9120.4750.9410.71398
1.86-1.943.80.516119660.8560.960.3020.5990.76398.2
1.94-2.033.80.322120030.9310.9820.190.3750.78398.4
2.03-2.133.60.202120350.9670.9920.1220.2370.83498.6
2.13-2.273.40.134121180.9780.9940.0870.1610.90298.7
2.27-2.443.50.093120760.9910.9980.0580.110.92599
2.44-2.693.90.067121370.9960.9990.0390.0780.98599.2
2.69-3.083.80.045121990.9980.9990.0260.0521.06299.4
3.08-3.883.60.032122610.99810.0190.0371.07299.4
3.88-303.60.025124550.99910.0150.0290.95799.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.135 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22943 1158 1 %RANDOM
Rwork0.18119 ---
obs0.18163 119970 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å2-0 Å2-0.33 Å2
2---0.46 Å20 Å2
3----1.36 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7409 0 2 860 8271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0146944
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.64610409
X-RAY DIFFRACTIONr_angle_other_deg1.3981.57816113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7122.656320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.106151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.841534
X-RAY DIFFRACTIONr_chiral_restr0.0780.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021676
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_it3.5263.6083990
X-RAY DIFFRACTIONr_mcbond_other3.5233.6083989
X-RAY DIFFRACTIONr_mcangle_it5.1335.3834977
X-RAY DIFFRACTIONr_mcangle_other5.1345.3844978
X-RAY DIFFRACTIONr_scbond_it4.343.9633652
X-RAY DIFFRACTIONr_scbond_other4.3393.9653653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.525.7435433
X-RAY DIFFRACTIONr_long_range_B_refined9.09643.3588396
X-RAY DIFFRACTIONr_long_range_B_other9.03942.8488194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 90 -
Rwork0.306 8581 -
obs--95.76 %

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