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- PDB-8sxp: Crystal structure of long neurotoxin from the venom of the king c... -

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Basic information

Entry
Database: PDB / ID: 8sxp
TitleCrystal structure of long neurotoxin from the venom of the king cobra (3FTx-L15) in complex with Fab of broadly neutralizing antibody 95Mat5
Components
  • 95Mat5 Fab heavy chain
  • 95Mat5 Fab light chain
  • Long neurotoxin 2
KeywordsTOXIN/IMMUNE SYSTEM / snake toxin / antibody / TOXIN / TOXIN-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 three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Ophiophagus hannah (king cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNguyen, T.K.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust221705 United Kingdom
CitationJournal: Sci Transl Med / Year: 2024
Title: Synthetic development of a broadly neutralizing antibody against snake venom long-chain neurotoxins
Authors: Khalek, I.S. / Senji Laxme, R.R. / Nguyen, Y.T.K. / Khochare, S. / Patel, R.N. / Woehl, J. / Smith, J.M. / Saye-Francisco, K. / Kim, Y. / Misson Mindrebo, L. / Tran, Q. / Kedzior, M. / Bore, ...Authors: Khalek, I.S. / Senji Laxme, R.R. / Nguyen, Y.T.K. / Khochare, S. / Patel, R.N. / Woehl, J. / Smith, J.M. / Saye-Francisco, K. / Kim, Y. / Misson Mindrebo, L. / Tran, Q. / Kedzior, M. / Bore, E. / Limbo, O. / Verma, M. / Stanfield, R.L. / Menzies, S.K. / Ainsworth, S. / Harrison, R.A. / Burton, D.R. / Sok, D. / Wilson, I.A. / Casewell, N.R. / Sunagar, K. / Jardine, J.G.
History
DepositionMay 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 95Mat5 Fab light chain
C: Long neurotoxin 2
H: 95Mat5 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)54,7093
Polymers54,7093
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-26 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.860, 42.443, 103.356
Angle α, β, γ (deg.)90.00, 103.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 95Mat5 Fab light chain


Mass: 23175.607 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: Protein Long neurotoxin 2


Mass: 7325.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiophagus hannah (king cobra) / Production host: Homo sapiens (human) / References: UniProt: P01386
#3: Antibody 95Mat5 Fab heavy chain


Mass: 24208.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.75 / Details: 100mM sodium citrate pH 3.75, and 26% PEG6000 / PH range: 3-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. obs: 10741 / % possible obs: 82.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 83.42 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.81
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.424 / Num. unique obs: 98 / CC1/2: 0.838 / Rpim(I) all: 0.354 / Rsym value: 0.424

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000v721.1data scaling
HKL-2000v721.1data reduction
PHENIX1.19.2-4158-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.49 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.32 534 4.97 %RANDOM
Rwork0.261 ---
obs0.2638 10741 82.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 0 3 3830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053926
X-RAY DIFFRACTIONf_angle_d0.8435341
X-RAY DIFFRACTIONf_dihedral_angle_d5.826548
X-RAY DIFFRACTIONf_chiral_restr0.048601
X-RAY DIFFRACTIONf_plane_restr0.009683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.489580.40691261X-RAY DIFFRACTION41
3.19-3.650.39831490.32052760X-RAY DIFFRACTION91
3.65-4.60.32131720.2623037X-RAY DIFFRACTION98
4.6-45.490.28061550.23023149X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -40.3292 Å / Origin y: -8.9531 Å / Origin z: 23.9739 Å
111213212223313233
T0.3018 Å2-0.0451 Å2-0.0878 Å2-0.2749 Å20.0293 Å2--0.2699 Å2
L2.0026 °20.6982 °2-0.9114 °2-2.1039 °2-0.19 °2--2.1467 °2
S0.0442 Å °-0.0676 Å °-0.0495 Å °-0.1272 Å °-0.0347 Å °0.1882 Å °0.1064 Å °-0.2203 Å °0.0028 Å °
Refinement TLS groupSelection details: all

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