5LY5 | pdb_00005ly5

Arcadin-1 from Pyrobaculum calidifontis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.230 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5LY5

This is version 1.1 of the entry. See complete history

Literature

Crenactin forms actin-like double helical filaments regulated by arcadin-2.

Izore, T.Kureisaite-Ciziene, D.McLaughlin, S.H.Lowe, J.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.21600
  • Primary Citation Related Structures: 
    5LY3, 5LY5, 5MW1

  • PubMed Abstract: 

    The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon Pyrobaculum calidifontis supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of crenactin and actin are similar, although their filament architectures were suggested to be different. Here we report that crenactin forms bona fide double helical filaments that show exceptional similarity to eukaryotic F-actin. With cryo-electron microscopy and helical reconstruction we solved the structure of the crenactin filament to 3.8 Å resolution. When forming double filaments, the 'hydrophobic plug' loop in crenactin rearranges. Arcadin-2, also encoded by the arcade gene cluster, binds tightly with its C-terminus to the hydrophobic groove of crenactin. Binding is reminiscent of eukaryotic actin modulators such as cofilin and thymosin β4 and arcadin-2 is a depolymeriser of crenactin filaments. Our work further supports the theory of shared ancestry of Eukaryotes and Crenarchaea.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 12.63 kDa 
  • Atom Count: 644 
  • Modeled Residue Count: 77 
  • Deposited Residue Count: 115 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
arcadin-1115Pyrobaculum calidifontisMutation(s): 0 
UniProt
Find proteins for Q8ZVH7 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2))
Explore Q8ZVH7 
Go to UniProtKB:  Q8ZVH7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZVH7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.230 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.051α = 90
b = 84.051β = 90
c = 61.33γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references