4Y0V

Structure of an ADP ribosylation factor from Entamoeba histolytica HM-1:IMSS bound to Mg-GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: experimental
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This is version 1.7 of the entry. See complete history


Literature

Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg(2+)-GDP.

Serbzhinskiy, D.A.Clifton, M.C.Sankaran, B.Staker, B.L.Edwards, T.E.Myler, P.J.

(2015) Acta Crystallogr F Struct Biol Commun 71: 594-599

  • DOI: https://doi.org/10.1107/S2053230X15004677
  • Primary Citation of Related Structures:  
    4Y0V, 4YLG

  • PubMed Abstract: 

    Entamoeba histolytica is the etiological agent of amebiasis, a diarrheal disease which causes amoebic liver abscesses and amoebic colitis. Approximately 50 million people are infected worldwide with E. histolytica. With only 10% of infected people developing symptomatic amebiasis, there are still an estimated 100,000 deaths each year. Because of the emergence of resistant strains of the parasite, it is necessary to find a treatment which would be a proper response to this challenge. ADP-ribosylation factor (ARF) is a member of the ARF family of GTP-binding proteins. These proteins are ubiquitous in eukaryotic cells; they generally associate with cell membranes and regulate vesicular traffic and intracellular signalling. The crystal structure of ARF1 from E. histolytica has been determined bound to magnesium and GDP at 1.8 Å resolution. Comparison with other structures of eukaryotic ARF proteins shows a highly conserved structure and supports the interswitch toggle mechanism of communicating the conformational state to partner proteins.


  • Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1
A, B
178Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI_073470EHI_137720
UniProt
Find proteins for C4LXL1 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
Explore C4LXL1 
Go to UniProtKB:  C4LXL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4LXL1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.54α = 90
b = 40.66β = 97.45
c = 78.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200025C

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2015-05-13
    Changes: Database references
  • Version 1.3: 2015-05-20
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.5: 2017-11-22
    Changes: Refinement description
  • Version 1.6: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.7: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description