8BEI

Structure of hexameric subcomplexes (Truncation Delta2-6) of the fractal citrate synthase from Synechococcus elongatus PCC7942


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Emergence of fractal geometries in the evolution of a metabolic enzyme.

Sendker, F.L.Lo, Y.K.Heimerl, T.Bohn, S.Persson, L.J.Mais, C.N.Sadowska, W.Paczia, N.Nussbaum, E.Del Carmen Sanchez Olmos, M.Forchhammer, K.Schindler, D.Erb, T.J.Benesch, J.L.P.Marklund, E.G.Bange, G.Schuller, J.M.Hochberg, G.K.A.

(2024) Nature 628: 894-900

  • DOI: https://doi.org/10.1038/s41586-024-07287-2
  • Primary Citation of Related Structures:  
    8AN1, 8BEI, 8BP7, 8RJK, 8RJL

  • PubMed Abstract: 

    Fractals are patterns that are self-similar across multiple length-scales 1 . Macroscopic fractals are common in nature 2-4 ; however, so far, molecular assembly into fractals is restricted to synthetic systems 5-12 . Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.


  • Organizational Affiliation

    Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate synthase
A, B, C, D, E
A, B, C, D, E, F
389Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_0612
UniProt
Find proteins for Q31QM5 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31QM5 
Go to UniProtKB:  Q31QM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31QM5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanySCHU3364/1-1
European Research Council (ERC)European Union101040472 EVOCATION

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Data collection, Database references