3P91

Crystal structure of Proliferating Cellular Nuclear Antigen from Entamoeba histolytica

• PDB DOI: https://doi.org/10.2210/pdb3P91/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-15 Released: 2011-06-01 
• Deposition Author(s): Lara-Gonzalez, S., Cardona-Felix, C.S., Brieba, L.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.193 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon.

Cardona-Felix, C.S., Lara-Gonzalez, S., Brieba, L.G.

(2011) Acta Crystallogr D Biol Crystallogr 67: 497-505

• PubMed: 21636889 
• DOI: https://doi.org/10.1107/S0907444911010547
• Primary Citation of Related Structures:  
  3P91


• PubMed Abstract: 
  

  Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.

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Organizational Affiliation: 

Grupo de Bioquímica Estructural, Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México.

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)

Macromolecule Content

• Total Structure Weight: 28.82 kDa 
• Atom Count: 1,839 
• Modelled Residue Count: 245 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A	265	Entamoeba histolytica	Mutation(s): 0  Gene Names: EHI_128450
UniProt
Find proteins for C4M9R9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4M9R9  Go to UniProtKB:  C4M9R9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.193 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.09	α = 90
b = 141.09	β = 90
c = 49.22	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Lara-Gonzalez, S., Cardona-Felix, C.S., Brieba, L.G.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description