5LY3

P. calidifontis crenactin in complex with arcadin-2 C-terminal peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin/actin family protein432Pyrobaculum calidifontisMutation(s): 0 
Gene Names: Pcal_1635
EC: 3.6.4
UniProt
Find proteins for A3MWN5 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
Explore A3MWN5 
Go to UniProtKB:  A3MWN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3MWN5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein16Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
Gene Names: Pcal_1636
UniProt
Find proteins for A3MWN6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
Explore A3MWN6 
Go to UniProtKB:  A3MWN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3MWN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.18α = 90
b = 70.909β = 104.21
c = 62.231γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description