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- PDB-8da1: Crystal structure of Krait alpha-neurotoxin in complex with Centi... -

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Basic information

Entry
Database: PDB / ID: 8da1
TitleCrystal structure of Krait alpha-neurotoxin in complex with Centi-3FTX-D09 antibody
Components
  • Alpha-bungarotoxin
  • Centi-3FTX-D09 Fab heavy chain
  • Centi-3FTX-D09 Fab light chain
KeywordsIMMUNE SYSTEM / ANTITOXIN/TOXIN / antivenom / 3-finger toxin / alpha-neurotoxin / long neurotoxin 1 / antibody / ANTITOXIN / ANTITOXIN-TOXIN complex
Function / homologySnake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / acetylcholine receptor inhibitor activity / ion channel regulator activity / Snake toxin-like superfamily / toxin activity / extracellular region / Alpha-bungarotoxin
Function and homology information
Biological speciesHomo sapiens (human)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsPletnev, S. / Verardi, R. / Tully, E.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: To Be Published
Title: Venom protection by antibody from a snakebite hyperimmune subject
Authors: Glanville, J. / Andrade, J. / Bellin, M. / Kim, S. / Pletnev, S. / Tsao, D. / Verardi, R. / Bedi, R. / Friede, T. / Tully, E. / Zhang, B. / Bylund, T. / Liu, T. / Kwong, P.D.
History
DepositionJun 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centi-3FTX-D09 Fab light chain
B: Centi-3FTX-D09 Fab heavy chain
I: Alpha-bungarotoxin


Theoretical massNumber of molelcules
Total (without water)56,4783
Polymers56,4783
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.326, 63.862, 77.437
Angle α, β, γ (deg.)90.000, 101.570, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Centi-3FTX-D09 Fab light chain


Mass: 23339.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Centi-3FTX-D09 Fab heavy chain


Mass: 25132.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: 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: 8005.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bungarus multicinctus (many-banded krait)
Production host: Homo sapiens (human) / References: UniProt: P60615
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% PEG 400, 5% PEG 3350, 0.1M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→30 Å / Num. obs: 19031 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.103 / Rrim(I) all: 0.27 / Χ2: 1.88 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.84.21.60118460.3060.8391.8171.57797.3
2.8-2.915.11.41818700.4080.6821.5811.59297.7
2.91-3.046.41.09918930.5930.4611.1941.70298.4
3.04-3.27.50.83719080.8170.3260.8991.86699.7
3.2-3.47.90.58718960.90.2230.6291.95599.7
3.4-3.667.80.40119300.9410.1530.432.03999.7
3.66-4.037.50.29119060.9450.1150.3141.97999
4.03-4.616.60.18819010.9560.0820.2071.96998.2
4.61-5.87.40.1619260.9720.0660.1741.92498.6
5.8-306.80.15719550.9690.0690.1721.89898.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model found by BALBES software using input sequence

Resolution: 2.67→29.51 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1020 5.36 %
Rwork0.1846 18000 -
obs0.1876 19020 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.5 Å2 / Biso mean: 74.4621 Å2 / Biso min: 38.71 Å2
Refinement stepCycle: final / Resolution: 2.67→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 0 2 3881
Biso mean---66.56 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.810.34711020.2781633173560
2.81-2.990.361270.28262682280997
2.99-3.220.34771750.239327212896100
3.22-3.540.28041660.205627092875100
3.54-4.050.23561530.17562743289699
4.05-5.10.20821520.15482712286498
5.1-29.510.20431450.17152800294598

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