5ZBT

Structure of legume lectin-like domain from Entamoeba histolytica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica

Khan, F.Suguna, K.

(2019) Acta Crystallogr F Struct Biol Commun 75: 197-204

  • DOI: https://doi.org/10.1107/S2053230X19000499
  • Primary Citation of Related Structures:  
    5ZBT

  • PubMed Abstract: 

    ERGIC-53-like proteins are type I membrane proteins that belong to the class of intracellular cargo receptors and are known to be indispensable for the intracellular transport of glycoproteins. They are implicated in transporting glycoproteins between the endoplasmic reticulum and the Golgi body. The crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica has been determined at 2.4 Å resolution. Although the overall structure of the domain resembles those of its mammalian and yeast orthologs (ERGIC-53 and Emp46, respectively), there are significant changes in the carbohydrate-binding site. A sequence-based search revealed the presence of several homologs of ERGIC-53 in different species of Entamoeba. This is the first report of the structural characterization of a member of this class of proteins from a protozoan and serves to further knowledge and understanding regarding the species-specific differences.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin-like protein251Entamoeba histolytica HM-1:IMSS-AMutation(s): 0 
Gene Names: EHI7A_000050
UniProt
Find proteins for N9T8S1 (Entamoeba histolytica HM-1:IMSS-A)
Explore N9T8S1 
Go to UniProtKB:  N9T8S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN9T8S1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.051α = 90
b = 57.174β = 90
c = 72.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
CRANK2phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references