5EPM

Ceratotoxin variant in complex with specific antibody Fab fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Engineering Highly Potent and Selective Microproteins against Nav1.7 Sodium Channel for Treatment of Pain.

Shcherbatko, A., Rossi, A., Foletti, D., Zhu, G., Bogin, O., Galindo Casas, M., Rickert, M., Hasa-Moreno, A., Bartsevich, V., Crameri, A., Steiner, A.R., Henningsen, R., Gill, A., Pons, J., Shelton, D.L., Rajpal, A., Strop, P.

(2016) J Biol Chem 291: 13974-13986

  • DOI: 10.1074/jbc.M116.725978
  • Primary Citation of Related Structures:  
    5EPM

  • PubMed Abstract: 

    • The prominent role of voltage-gated sodium channel 1.7 (Nav1.7) in nociception was revealed by remarkable human clinical and genetic evidence. Development of potent and subtype-selective inhibitors of this ion channel is crucial for obtaining therapeutically useful analgesic compounds ...

    The prominent role of voltage-gated sodium channel 1.7 (Nav1.7) in nociception was revealed by remarkable human clinical and genetic evidence. Development of potent and subtype-selective inhibitors of this ion channel is crucial for obtaining therapeutically useful analgesic compounds. Microproteins isolated from animal venoms have been identified as promising therapeutic leads for ion channels, because they naturally evolved to be potent ion channel blockers. Here, we report the engineering of highly potent and selective inhibitors of the Nav1.7 channel based on tarantula ceratotoxin-1 (CcoTx1). We utilized a combination of directed evolution, saturation mutagenesis, chemical modification, and rational drug design to obtain higher potency and selectivity to the Nav1.7 channel. The resulting microproteins are highly potent (IC50 to Nav1.7 of 2.5 nm) and selective. We achieved 80- and 20-fold selectivity over the closely related Nav1.2 and Nav1.6 channels, respectively, and the IC50 on skeletal (Nav1.4) and cardiac (Nav1.5) sodium channels is above 3000 nm The lead molecules have the potential for future clinical development as novel therapeutics in the treatment of pain.

    Organizational Affiliation: 

    From the Rinat Laboratories, Pfizer Inc., South San Francisco, California 94080, pavel.strop@bms.com.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab fragment heavy chainA, E219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab fragment light chainB, F218Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-theraphotoxin-Cm1aC, D33Ceratogyrus marshalliMutation(s): 9 
UniProt
Find proteins for P84507 (Ceratogyrus marshalli)
Explore P84507 
Go to UniProtKB:  P84507
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA		A, EL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.322α = 90
b = 98.438β = 90
c = 107.35γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2016-07-13
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description