3M1X | pdb_00003m1x

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, rhomobohedral form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.131 (Depositor), 0.140 (DCC) 
  • R-Value Work: 
    0.106 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.107 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of the putative endoribonuclease L-PSP from Entamoeba histolytica.

Ojuromi, O.T.Giwa, A.O.Gardberg, A.Subramanian, S.Myler, P.J.Abendroth, J.Staker, B.Asojo, O.A.

(2025) Acta Crystallogr F Struct Biol Commun 81: 226-234

  • DOI: https://doi.org/10.1107/S2053230X25003875
  • Primary Citation of Related Structures:  
    3M1X, 3M4S, 3MQW

  • PubMed Abstract: 

    Entamoeba histolytica causes amebiasis, a neglected disease that kills ∼100 000 people globally each year. Due to emerging drug resistance, E. histolytica is one of the target organisms for structure-based drug discovery by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Purification, crystallization and three structures of the putative drug target endoribonuclease L-PSP from E. histolytica (EhL-PSP) are presented. EhL-PSP has a two-layer α/β-sandwich with structural homology to endoribonuclease L-PSP. All three structures reveal the prototypical YjgF/YER057c/UK114 family trimer topology with accessible allosteric active sites. Citrate molecules from the crystallization solution are bound to the allosteric site in two of the three reported structures. The large allosteric site of EhL-PSP is well conserved with bacterial YjgF/YER057c/UK114 family members and could be targeted for inhibition, drug discovery or repurposing.


  • Organizational Affiliation
    • Zoology and Environmental Biology, Lagos State University, Nigeria.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative Endoribonuclease L-PSP148Entamoeba histolytica HM-1:IMSSMutation(s): 0 
Gene Names: EHI_087570
UniProt
Find proteins for C4LXT9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
Explore C4LXT9 
Go to UniProtKB:  C4LXT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4LXT9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MHO
Query on MHO
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.131 (Depositor), 0.140 (DCC) 
  • R-Value Work:  0.106 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.107 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.546α = 90
b = 78.546β = 90
c = 89.18γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary
  • Version 1.4: 2025-12-24
    Changes: Database references