6MRQ

Structure of ToPI1 inhibitor from Tityus obscurus scorpion venom in complex with trypsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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This is version 1.3 of the entry. See complete history


Literature

Head-to-Tail Cyclization after Interaction with Trypsin: A Scorpion Venom Peptide that Resembles Plant Cyclotides.

Mourao, C.B.F.Brand, G.D.Fernandes, J.P.C.Prates, M.V.Bloch Jr., C.Barbosa, J.A.R.G.Freitas, S.M.Restano-Cassulini, R.Possani, L.D.Schwartz, E.F.

(2020) J Med Chem 63: 9500-9511

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00686
  • Primary Citation of Related Structures:  
    6MRQ

  • PubMed Abstract: 

    Peptidase inhibitors (PIs) have been broadly studied due to their wide therapeutic potential for human diseases. A potent trypsin inhibitor from Tityus obscurus scorpion venom was characterized and named ToPI1, with 33 amino acid residues and three disulfide bonds. The X-ray structure of the ToPI1:trypsin complex, in association with the mass spectrometry data, indicate a sequential set of events: the complex formation with the inhibitor Lys 32 in the trypsin S1 pocket, the inhibitor C-terminal residue Ser 33 cleavage, and the cyclization of ToPI1 via a peptide bond between residues Ile 1 and Lys 32 . Kinetic and thermodynamic characterization of the complex was obtained. ToPI1 shares no sequence similarity with other PIs characterized to date and is the first PI with CS-α/β motif described from animal venoms. In its cyclic form, it shares structural similarities with plant cyclotides that also inhibit trypsin. These results bring new insights for studies with venom compounds, PIs, and drug design.


  • Organizational Affiliation

    Neuropharma Lab, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brası́lia, Brasília-DF 70910-900, Brazil.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic trypsin237Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
inhibitor from Tityus obscurus scorpion venom (TopI1)B [auth I]32TityusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.817α = 90
b = 59.02β = 90
c = 79.085γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil407625/2013-5
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil309054/2014-1
Fundacao de Apoio a Pesquisa do Distrito Federal (FAPDF)Brazil193.001.760/2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-09-23
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description