5LY3 | pdb_00005ly3

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

• PDB DOI: https://doi.org/10.2210/pdb5LY3/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Pyrobaculum calidifontis, Pyrobaculum calidifontis JCM 11548
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-23 Released: 2016-11-30 
• Deposition Author(s): Izore, T., Lowe, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.200 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

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

• PubMed: 27852434 
• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.7 kDa 
• Atom Count: 3,867 
• Modeled Residue Count: 443 
• Deposited Residue Count: 448 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin/actin family protein	A	432	Pyrobaculum calidifontis	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein	B	16	Pyrobaculum calidifontis JCM 11548	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	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 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.18	α = 90
b = 70.909	β = 104.21
c = 62.231	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Izore, T., Lowe, J.

Revision History  

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