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- PDB-8d9y: Crystal structure of Taipan alpha-neurotoxin in complex with Cent... -

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Basic information

Entry
Database: PDB / ID: 8d9y
TitleCrystal structure of Taipan alpha-neurotoxin in complex with Centi-3FTX-D09 antibody
Components
  • (Centi-3FTX-D09 Fab ...) x 2
  • Long neurotoxin 1
KeywordsIMMUNE SYSTEM / ANTITOXIN/TOXIN / antivenom / 3-finger toxin / alpha-neurotoxin / long neurotoxin 1 / antibody / ANTITOXIN / ANTITOXIN-TOXIN complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin/toxin-like / Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Snake toxin-like superfamily
Similarity search - Domain/homology
Chem-PG6 / Long neurotoxin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Oxyuranus scutellatus scutellatus (Australian taipan)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
C: Centi-3FTX-D09 Fab light chain
D: Centi-3FTX-D09 Fab heavy chain
E: Centi-3FTX-D09 Fab light chain
F: Centi-3FTX-D09 Fab heavy chain
G: Centi-3FTX-D09 Fab light chain
H: Centi-3FTX-D09 Fab heavy chain
I: Long neurotoxin 1
J: Long neurotoxin 1
K: Long neurotoxin 1
L: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,30616
Polymers225,51512
Non-polymers7914
Water17,150952
1
A: Centi-3FTX-D09 Fab light chain
B: Centi-3FTX-D09 Fab heavy chain
I: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6174
Polymers56,3793
Non-polymers2381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Centi-3FTX-D09 Fab light chain
D: Centi-3FTX-D09 Fab heavy chain
J: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8395
Polymers56,3793
Non-polymers4612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Centi-3FTX-D09 Fab light chain
F: Centi-3FTX-D09 Fab heavy chain
K: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4714
Polymers56,3793
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Centi-3FTX-D09 Fab light chain
H: Centi-3FTX-D09 Fab heavy chain
L: Long neurotoxin 1


Theoretical massNumber of molelcules
Total (without water)56,3793
Polymers56,3793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.808, 87.228, 101.302
Angle α, β, γ (deg.)109.290, 104.260, 106.480
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.996537, -0.001453, 0.083136), (0.002797, -0.999867, 0.016052), (0.083101, 0.016229, 0.996409)5.4028, -37.034489, 0.09458
3given(-0.602013, -0.482281, -0.636385), (-0.336192, 0.875998, -0.345836), (0.724262, 0.005749, -0.689501)-8.90966, 66.171997, 33.518009
4given(0.474807, 0.645264, -0.598492), (0.466386, -0.761176, -0.45066), (-0.746353, -0.065152, -0.662354)85.15123, -4.70046, -8.14223

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Components

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Protein , 1 types, 4 molecules IJKL

#3: Protein
Long neurotoxin 1 / LNTX-1


Mass: 7906.118 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxyuranus scutellatus scutellatus (Australian taipan)
Production host: Homo sapiens (human) / References: UniProt: A8HDK9

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Antibody , 2 types, 8 molecules ACEGBDFH

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


Mass: 23339.740 Da / Num. of mol.: 4
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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 956 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100mM Sodium Acetate pH 5.5, 14% PEG8000, 2.65% PEG 400, 500mM NaCl

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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: 2.2→30 Å / Num. obs: 99175 / % possible obs: 86.8 % / Redundancy: 2 % / Biso Wilson estimate: 35.97 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.065 / Rrim(I) all: 0.099 / Χ2: 0.738 / Net I/σ(I): 6.4 / Num. measured all: 200208
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2820.486750.7620.3460.5310.44776.1
2.28-2.3720.31595980.8530.2760.420.46483.6
2.37-2.4820.26899510.8920.2370.3590.47987.6
2.48-2.6120.21798450.9210.1930.2910.52786.1
2.61-2.7720.16997930.9450.1520.2280.64285.8
2.77-2.992.10.126107010.9680.1130.170.7493.6
2.99-3.292.10.089105740.9810.0790.1190.88792.4
3.29-3.7620.065100590.9860.0580.0871.02388.3
3.76-4.7320.04599390.9930.0390.061.05287
4.73-3020.042100400.990.0370.0561.03187.7

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
SCALEPACKdata scaling
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: 2.2→29.54 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1954 1.99 %RANDOM
Rwork0.2093 96308 --
obs0.2103 98262 86.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.39 Å2 / Biso mean: 51.9086 Å2 / Biso min: 16.11 Å2
Refinement stepCycle: final / Resolution: 2.2→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15145 0 52 955 16152
Biso mean--63.31 47.94 -
Num. residues----1995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.34771240.33125936606075
2.26-2.320.28991330.30256340647380
2.32-2.380.34471420.29156686682885
2.38-2.460.30241490.28636958710787
2.46-2.550.31011360.2756923705987
2.55-2.650.35191360.26216431656781
2.65-2.770.31241420.24547162730490
2.77-2.920.29351450.22637453759894
2.92-3.10.3191380.2297398753693
3.1-3.340.26121750.21327217739292
3.34-3.670.25331340.19267026716088
3.67-4.20.21931250.17896717684284
4.21-5.290.18571360.15367105724189
5.29-29.540.2521390.18116956709588

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