3MQW | pdb_00003mqw

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica with higher solvent content and an ordered N-terminal tag

• PDB DOI: https://doi.org/10.2210/pdb3MQW/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-28 Released: 2010-05-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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

• PubMed: 40314238 
• DOI: https://doi.org/10.1107/S2053230X25003875
• Primary Citation 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.

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Organizational Affiliation: 
• Zoology and Environmental Biology, Lagos State University, Nigeria.
Freelance Structural Biology Consultant, Greater Boston Area, Massachusetts, USA.
Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA.
Dartmouth Cancer Center, One Medical Center Drive, Lebanon, NH 03756, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.28 kDa 
• Atom Count: 6,943 
• Modeled Residue Count: 817 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Endoribonuclease L-PSP	A, B, C, D, E, F	148	Entamoeba histolytica	Mutation(s): 0  Gene Names: EHI_087570, HM-1:IMSS
UniProt
Find proteins for C4LXT9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LXT9  Go to UniProtKB:  C4LXT9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	G [auth A], I [auth B], M [auth C], Q [auth D], U [auth E]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4	J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], T [auth E], W [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], L [auth B], P [auth C], S [auth D], V [auth E], X [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33MQW

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84	α = 90
b = 99.72	β = 90
c = 106.1	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-05-12
  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: 2025-12-24
  Changes: Database references, Structure summary