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- PDB-4v1d: Ternary complex among two human derived single chain antibody fra... -

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Basic information

Entry
Database: PDB / ID: 4v1d
TitleTernary complex among two human derived single chain antibody fragments and Cn2 toxin from scorpion Centruroides noxius.
Components
  • (SINGLE CHAIN ANTIBODY FRAGMENT LR, ...) x 2
  • (SINGLE CHAIN ANTIBODY FRAGMENT RU1, ...) x 2
  • BETA-MAMMAL TOXIN CN2
KeywordsTOXIN/IMMUNE SYSTEM / TOXIN-IMMUNE SYSTEM COMPLEX / HUMAN SCFV / SCORPION VENOM NEUTRALIZATION / DIRECTED EVOLUTION / CN2 TOXIN.
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-mammal toxin Cn2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
CENTRUROIDES NOXIUS (Mexican scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRiano-Umbarila, L. / Serrano-Posada, H. / Rojas-Trejo, S. / Rudino-Pinera, E. / Becerril, B.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Optimal Neutralization of Centruroides Noxius Venom is Understood Through a Structural Complex between Two Antibody Fragments and the Cn2 Toxin.
Authors: Riano-Umbarila, L. / Ledezma-Candanoza, L.M. / Serrano-Posada, H. / Fernandez-Taboada, G. / Olamendi-Portugal, T. / Rojas-Trejo, S. / Gomez-Ramirez, I.V. / Rudino-Pinera, E. / Possani, L.D. / Becerril, B.
History
DepositionSep 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SINGLE CHAIN ANTIBODY FRAGMENT LR, HEAVY CHAIN
B: SINGLE CHAIN ANTIBODY FRAGMENT LR, LIGHT CHAIN
C: BETA-MAMMAL TOXIN CN2
D: SINGLE CHAIN ANTIBODY FRAGMENT RU1, HEAVY CHAIN
E: SINGLE CHAIN ANTIBODY FRAGMENT RU1, LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)64,3165
Polymers64,3165
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.576, 74.643, 140.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Antibody , 4 types, 4 molecules ABDE

#1: Antibody SINGLE CHAIN ANTIBODY FRAGMENT LR, HEAVY CHAIN


Mass: 12581.890 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
#2: Antibody SINGLE CHAIN ANTIBODY FRAGMENT LR, LIGHT CHAIN


Mass: 15418.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
#4: Antibody SINGLE CHAIN ANTIBODY FRAGMENT RU1, HEAVY CHAIN


Mass: 13556.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
#5: Antibody SINGLE CHAIN ANTIBODY FRAGMENT RU1, LIGHT CHAIN


Mass: 15151.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1

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Protein / Non-polymers , 2 types, 7 molecules C

#3: Protein BETA-MAMMAL TOXIN CN2 / / TOXIN 2 / TOXIN II.9.2.2


Mass: 7607.728 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-82 / Source method: isolated from a natural source / Source: (natural) CENTRUROIDES NOXIUS (Mexican scorpion) / References: UniProt: P01495
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.86 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M SPG PH 8.5, 25%(W/V) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 24, 2013
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→39 Å / Num. obs: 9184 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 44.67 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.5
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YC1

2yc1


Resolution: 3.1→38.214 Å / SU ML: 0.07 / σ(F): 1.91 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 439 4.8 %
Rwork0.1848 --
obs0.1871 9184 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→38.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 0 6 4024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064142
X-RAY DIFFRACTIONf_angle_d1.1245599
X-RAY DIFFRACTIONf_dihedral_angle_d14.5051478
X-RAY DIFFRACTIONf_chiral_restr0.047590
X-RAY DIFFRACTIONf_plane_restr0.004731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.54830.27351330.2182860X-RAY DIFFRACTION100
3.5483-4.46940.22551370.17572885X-RAY DIFFRACTION100
4.4694-38.21640.20931690.17333000X-RAY DIFFRACTION100

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