5NL6 | pdb_00005nl6

The crystal structure of the two spectrin repeat domains from Entamoeba histolytica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5NL6

This is version 1.2 of the entry. See complete history

Literature

Calcium modulates the domain flexibility and function of an alpha-actinin similar to the ancestral alpha-actinin.

Pinotsis, N.Zielinska, K.Babuta, M.Arolas, J.L.Kostan, J.Khan, M.B.Schreiner, C.Salmazo, A.Ciccarelli, L.Puchinger, M.Gkougkoulia, E.A.Ribeiro Jr., E.A.Marlovits, T.C.Bhattacharya, A.Djinovic-Carugo, K.

(2020) Proc Natl Acad Sci U S A 117: 22101-22112

  • DOI: https://doi.org/10.1073/pnas.1917269117
  • Primary Citation Related Structures: 
    5NL6, 5NL7, 6SL2, 6SL3, 6SL7

  • PubMed Abstract: 

    The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin-binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca 2+ in nonmuscle cells. Here we report the mechanism of Ca 2+ -mediated regulation of Entamoeba histolytica α-actinin-2 ( Eh Actn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca 2+ -free and Ca 2+ -bound Eh Actn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the Eh Actn2 CaMD for Ca 2+ , binding of which can only be regulated in the presence of physiological concentrations of Mg 2+ Ca 2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin-binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that Eh Actn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.


  • Organizational Affiliation
    • Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, A-1030 Vienna, Austria.

Macromolecule Content 

  • Total Structure Weight: 55.47 kDa 
  • Atom Count: 4,196 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 490 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calponin domain family protein
A, B
245Entamoeba histolytica HM-1:IMSSMutation(s): 0 
Gene Names: EHI7A_134780
UniProt
Find proteins for N9TIJ7 (Entamoeba histolytica HM-1:IMSS-A)
Explore N9TIJ7 
Go to UniProtKB:  N9TIJ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN9TIJ7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.084α = 90
b = 59.978β = 90
c = 187.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Structure summary