7PJE | pdb_00007pje

Inhibiting parasite proliferation using a rationally designed anti-tubulin agent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.213 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Inhibiting parasite proliferation using a rationally designed anti-tubulin agent.

Gaillard, N.Sharma, A.Abbaali, I.Liu, T.Shilliday, F.Cook, A.D.Ehrhard, V.Bangera, M.Roberts, A.J.Moores, C.A.Morrissette, N.Steinmetz, M.O.

(2021) EMBO Mol Med 13: e13818-e13818

  • DOI: https://doi.org/10.15252/emmm.202013818
  • Primary Citation Related Structures: 
    7PJE, 7PJF

  • PubMed Abstract: 

    Infectious diseases caused by apicomplexan parasites remain a global public health threat. The presence of multiple ligand-binding sites in tubulin makes this protein an attractive target for anti-parasite drug discovery. However, despite remarkable successes as anti-cancer agents, the rational development of protozoan parasite-specific tubulin drugs has been hindered by a lack of structural and biochemical information on protozoan tubulins. Here, we present atomic structures for a protozoan tubulin and microtubule and delineate the architectures of apicomplexan tubulin drug-binding sites. Based on this information, we rationally designed the parasite-specific tubulin inhibitor parabulin and show that it inhibits growth of parasites while displaying no effects on human cells. Our work presents for the first time the rational design of a species-specific tubulin drug providing a framework to exploit structural differences between human and protozoa tubulin variants enabling the development of much-needed, novel parasite inhibitors.


  • Organizational Affiliation
    • Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 233.55 kDa 
  • Atom Count: 16,359 
  • Modeled Residue Count: 1,946 
  • Deposited Residue Count: 2,094 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha chainA,
D [auth C]
449Tetrahymena thermophilaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P41351 (Tetrahymena thermophila)
Explore P41351 
Go to UniProtKB:  P41351
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41351
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chainB,
E [auth D]
443Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for P41352 (Tetrahymena thermophila)
Explore P41352 
Go to UniProtKB:  P41352
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41352
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Darpin D1C [auth F],
F [auth E]
155synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.13α = 90
b = 183.92β = 92.44
c = 118.323γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novartis FreeNovationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 2.0: 2021-11-03
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Refinement description