5YEE

Crystal structure of LokiProfilin1/Rabbit Actin Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Genomes of Asgard archaea encode profilins that regulate actin.

Akil, C.Robinson, R.C.

(2018) Nature 562: 439-443

  • DOI: 10.1038/s41586-018-0548-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The origin of the eukaryotic cell is unresolved <sup>1,2 </sup>. Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea <sup>3,4 </sup>, consistent with the hypothesis that the eukaryotic cell e ...

    The origin of the eukaryotic cell is unresolved 1,2 . Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea 3,4 , consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of the hallmarks of the eukaryotic cell 5 . Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago 6 . Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation of actin filaments, an effect that is reduced in the presence of phospholipids. Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard archaea possess a primordial, polar, profilin-regulated actin system, which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic-like genes involved in membrane-trafficking and endocytosis 3,4 , imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.


    Organizational Affiliation

    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. rrobinson@imcb.a-star.edu.sg.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan. rrobinson@imcb.a-star.edu.sg.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore, Singapore. rrobinson@imcb.a-star.edu.sg.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, alpha skeletal muscle
B
377Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1 (ACTA)
Find proteins for P68135 (Oryctolagus cuniculus)
Go to Gene View: ACTA1
Go to UniProtKB:  P68135
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A
136Lokiarchaeum sp. (strain GC14_75)Mutation(s): 0 
Find proteins for A0A0F8V8L2 (Lokiarchaeum sp. (strain GC14_75))
Go to UniProtKB:  A0A0F8V8L2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
LAB
Query on LAB

Download SDF File 
Download CCD File 
B
LATRUNCULIN B
C20 H29 N O5 S
NSHPHXHGRHSMIK-JRIKCGFMSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.312α = 90.00
b = 126.209β = 97.89
c = 53.862γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references, Structure summary
  • Version 1.3: 2018-10-31
    Type: Data collection, Database references