4V1D | pdb_00004v1d

Ternary complex among two human derived single chain antibody fragments and Cn2 toxin from scorpion Centruroides noxius.

• PDB DOI: https://doi.org/10.2210/pdb4V1D/pdb

• Classification: TOXIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Centruroides noxius
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2014-09-25 Released: 2015-10-07 
• Deposition Author(s): Riano-Umbarila, L., Serrano-Posada, H., Rojas-Trejo, S., Rudino-Pinera, E., Becerril, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Optimal Neutralization of Centruroides Noxius Venom is Understood Through a Structural Complex between Two Antibody Fragments and the Cn2 Toxin.

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.

(2016) J Biological Chem 291: 1619

• PubMed: 26589800 
• DOI: https://doi.org/10.1074/jbc.M115.685297
• Primary Citation Related Structures: 
  4V1D


• PubMed Abstract: 
  

  The current trend of using recombinant antibody fragments in research to develop novel antidotes against scorpion stings has achieved excellent results. The polyclonal character of commercial antivenoms, obtained through the immunization of animals and which contain several neutralizing antibodies that recognize different epitopes on the toxins, guarantees the neutralization of the venoms. To avoid the use of animals, we aimed to develop an equivalent recombinant antivenom composed of a few neutralizing single chain antibody fragments (scFvs) that bind to two different epitopes on the scorpion toxins. In this study, we obtained scFv RU1 derived from scFv C1. RU1 showed a good capacity to neutralize the Cn2 toxin and whole venom of the scorpion Centruroides noxius. Previously, we had produced scFv LR, obtained from a different parental fragment (scFv 3F). LR also showed a similar neutralizing capacity. The simultaneous administration of both scFvs resulted in improved protection, which was translated as a rapid recovery of previously poisoned animals. The crystallographic structure of the ternary complex scFv LR-Cn2-scFv RU1 allowed us to identify the areas of interaction of both scFvs with the toxin, which correspond to non-overlapping sites. The epitope recognized by scFv RU1 seems to be related to a greater efficiency in the neutralization of the whole venom. In addition, the structural analysis of the complex helped us to explain the cross-reactivity of these scFvs and how they neutralize the venom.

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Organizational Affiliation: 
• From the Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, Morelos 62250, México and.
the Laboratorio de Bioingeniería, Universidad de Colima, Km. 9 carretera Coquimatlán-Colima, C.P. 28400 Coquimatlán, Colima, México.
From the Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, Morelos 62250, México and. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.32 kDa 
• Atom Count: 4,046 
• Modeled Residue Count: 528 
• Deposited Residue Count: 602 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SINGLE CHAIN ANTIBODY FRAGMENT LR, HEAVY CHAIN	A	117	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SINGLE CHAIN ANTIBODY FRAGMENT LR, LIGHT CHAIN	B	146	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-MAMMAL TOXIN CN2	C	66	Centruroides noxius	Mutation(s): 0
UniProt
Find proteins for P01495 (Centruroides noxius) Explore P01495  Go to UniProtKB:  P01495

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SINGLE CHAIN ANTIBODY FRAGMENT RU1, HEAVY CHAIN	D	124	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SINGLE CHAIN ANTIBODY FRAGMENT RU1, LIGHT CHAIN	E	149	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.576	α = 90
b = 74.643	β = 90
c = 140.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Riano-Umbarila, L., Serrano-Posada, H., Rojas-Trejo, S., Rudino-Pinera, E., Becerril, B.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references
• Version 1.2: 2016-02-03
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary