8BEI | pdb_00008bei

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

• PDB DOI: https://doi.org/10.2210/pdb8BEI/pdb
• EM Map EMD-16004: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-21 Released: 2024-02-28 
• Deposition Author(s): Lo, Y.K., Bohn, S., Sendker, F.L., Schuller, J.M., Hochberg, G.
• Funding Organization(s): Max Planck Society, German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

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

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

• PubMed: 38600380 
• DOI: https://doi.org/10.1038/s41586-024-07287-2
• Primary Citation 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.

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Organizational Affiliation: 
• Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany.
Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
Department of Chemistry, University of Oxford, Oxford, UK.
Kavli Institute for Nanoscience Discovery, Oxford, UK.
Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany.
MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Department of Biology, Philipps-University Marburg, Marburg, Germany.
Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany. [e-mail].
Department of Chemistry, Philipps-University Marburg, Marburg, Germany. [e-mail].
Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].
Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany. [e-mail].
Department of Chemistry, Philipps-University Marburg, Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 263.28 kDa 
• Atom Count: 16,578 
• Modeled Residue Count: 2,100 
• Deposited Residue Count: 2,334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A, B, C, D, E, F	389	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(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

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Lo, Y.K., Bohn, S., Sendker, F.L., Schuller, J.M., Hochberg, G.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	SCHU3364/1-1
European Research Council (ERC)	European Union	101040472 EVOCATION

Revision History  

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