8AJ7 | pdb_00008aj7

Kunitz domain of Amblyomin-X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.297 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural and functional properties of the Kunitz-type and C-terminal domains of Amblyomin-X supporting its antitumor activity.

Morais, K.L.P.Ciccone, L.Stura, E.Alvarez-Flores, M.P.Mourier, G.Driessche, M.V.Sciani, J.M.Iqbal, A.Kalil, S.P.Pereira, G.J.Marques-Porto, R.Cunegundes, P.Juliano, L.Servent, D.Chudzinski-Tavassi, A.M.

(2023) Front Mol Biosci 10: 1072751-1072751

  • DOI: https://doi.org/10.3389/fmolb.2023.1072751
  • Primary Citation of Related Structures:  
    8AJ7

  • PubMed Abstract: 

    Amblyomin-X is a Kunitz-type FXa inhibitor identified through the transcriptome analysis of the salivary gland from Amblyomma sculptum tick. This protein consists of two domains of equivalent size, triggers apoptosis in different tumor cell lines, and promotes regression of tumor growth, and reduction of metastasis. To study the structural properties and functional roles of the N-terminal (N-ter) and C-terminal (C-ter) domains of Amblyomin-X, we synthesized them by solid-phase peptide synthesis, solved the X-Ray crystallographic structure of the N-ter domain, confirming its Kunitz-type signature, and studied their biological properties. We show here that the C-ter domain is responsible for the uptake of Amblyomin-X by tumor cells and highlight the ability of this domain to deliver intracellular cargo by the strong enhancement of the intracellular detection of molecules with low cellular-uptake efficiency (p15) after their coupling with the C-ter domain. In contrast, the N-ter Kunitz domain of Amblyomin-X is not capable of crossing through the cell membrane but is associated with tumor cell cytotoxicity when it is microinjected into the cells or fused to TAT cell-penetrating peptide. Additionally, we identify the minimum length C-terminal domain named F2C able to enter in the SK-MEL-28 cells and induces dynein chains gene expression modulation, a molecular motor that plays a role in the uptake and intracellular trafficking of Amblyomin-X.


  • Organizational Affiliation
    • Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kunitz domain of Amblyomin-X
A, B
58Amblyomma sculptumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.297 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.54α = 90
b = 46.09β = 90
c = 76.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Alternative Energies and Atomic Energy Commission (CEA)FranceOSLOC104BUTADS

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary