8S9E | pdb_00008s9e

Solution structure of jarastatin (rJast), a disintegrin from Bothrops jararaca


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 8S9E

This is version 1.2 of the entry. See complete history

Literature

Toward the mechanism of jarastatin (rJast) inhibition of the integrin alpha V beta 3.

Vasconcelos, A.A.Estrada, J.C.Caruso, I.P.Kurtenbach, E.Zingali, R.B.Almeida, F.C.L.

(2024) Int J Biol Macromol 255: 128078-128078

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.128078
  • Primary Citation Related Structures: 
    8S9E

  • PubMed Abstract: 

    Disintegrins are a family of cysteine-rich small proteins that were first identified in snake venom. The high divergence of disintegrins gave rise to a plethora of functions, all related to the interaction with integrins. Disintegrins evolved to interact selectively with different integrins, eliciting many physiological outcomes and being promising candidates for the therapy of many pathologies. We used NMR to determine the structure and dynamics of the recombinant disintegrin jarastatin (rJast) and its interaction with the cancer-related integrin αVβ3. rJast displayed the canonical fold of a medium-sized disintegrin and showed complex dynamic in multiple timescales. We used NMR experiments to map the interaction of rJast with αVβ3, and molecular docking followed by molecular dynamics (MD) simulation to describe the first structural model of a disintegrin/integrin complex. We showed that not only the RGD loop participates in the interaction, but also the N-terminal domain. rJast plasticity was essential for the interaction with αVβ3 and correlated with the main modes of motion depicted in the MD trajectories. In summary, our study provides novel structural insights that enhance our comprehension of the mechanisms underlying disintegrin functionality.


  • Organizational Affiliation
    • Laboratório de RMN de Biomoléculas, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.

Macromolecule Content 

  • Total Structure Weight: 7.76 kDa 
  • Atom Count: 529 
  • Modeled Residue Count: 73 
  • Deposited Residue Count: 73 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Disintegrin jarastatin73Bothrops jararacaMutation(s): 0 
UniProt
Find proteins for Q0NZX5 (Bothrops jararaca)
Explore Q0NZX5 
Go to UniProtKB:  Q0NZX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0NZX5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil313517/2021-5

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Structure summary