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- PDB-8bei: Structure of hexameric subcomplexes (Truncation Delta2-6) of the ... -

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Basic information

Entry
Database: PDB / ID: 8bei
TitleStructure of hexameric subcomplexes (Truncation Delta2-6) of the fractal citrate synthase from Synechococcus elongatus PCC7942
ComponentsCitrate synthase
KeywordsTRANSFERASE / Fractal complex
Function / homology
Function and homology information


: / tricarboxylic acid cycle / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsLo, Y.K. / Bohn, S. / Sendker, F.L. / Schuller, J.M. / Hochberg, G.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SCHU3364/1-1 Germany
European Research Council (ERC)101040472 EVOCATIONEuropean Union
CitationJournal: Nature / Year: 2024
Title: Emergence of fractal geometries in the evolution of a metabolic enzyme.
Authors: Franziska L Sendker / Yat Kei Lo / Thomas Heimerl / Stefan Bohn / Louise J Persson / Christopher-Nils Mais / Wiktoria Sadowska / Nicole Paczia / Eva Nußbaum / María Del Carmen Sánchez ...Authors: Franziska L Sendker / Yat Kei Lo / Thomas Heimerl / Stefan Bohn / Louise J Persson / Christopher-Nils Mais / Wiktoria Sadowska / Nicole Paczia / Eva Nußbaum / María Del Carmen Sánchez Olmos / Karl Forchhammer / Daniel Schindler / Tobias J Erb / Justin L P Benesch / Erik G Marklund / Gert Bange / Jan M Schuller / Georg K A Hochberg /
Abstract: Fractals are patterns that are self-similar across multiple length-scales. Macroscopic fractals are common in nature; however, so far, molecular assembly into fractals is restricted to synthetic ...Fractals are patterns that are self-similar across multiple length-scales. Macroscopic fractals are common in nature; however, so far, molecular assembly into fractals is restricted to synthetic systems. 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.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)263,2796
Polymers263,2796
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Citrate synthase


Mass: 43879.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: Synpcc7942_0612 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31QM5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
PHENIXdev_4336:refinement
UCSF ChimeraX1.3/v9model building
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 774026 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217064
ELECTRON MICROSCOPYf_angle_d0.47123196
ELECTRON MICROSCOPYf_dihedral_angle_d3.5382334
ELECTRON MICROSCOPYf_chiral_restr0.0382580
ELECTRON MICROSCOPYf_plane_restr0.0063024

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