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- PDB-8rjk: Pseudoatomic model of a second-order Sierpinski triangle formed b... -

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Basic information

Entry
Database: PDB / ID: 8rjk
TitlePseudoatomic model of a second-order Sierpinski triangle formed by the citrate synthase from Synechococcus elongatus
ComponentsCitrate synthase
KeywordsTRANSFERASE / Fractal complex
Function / homology
Function and homology information


citrate (Si)-synthase activity / 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: 5.91 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
DepositionDec 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Citrate synthase
1: Citrate synthase
2: Citrate synthase
3: Citrate synthase
4: Citrate synthase
5: Citrate synthase
6: Citrate synthase
7: Citrate synthase
8: Citrate synthase
9: Citrate synthase
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase
G: Citrate synthase
H: Citrate synthase
I: Citrate synthase
J: Citrate synthase
K: Citrate synthase
L: Citrate synthase
M: Citrate synthase
N: Citrate synthase
O: Citrate synthase
P: Citrate synthase
Q: Citrate synthase
R: Citrate synthase
S: Citrate synthase
T: Citrate synthase
U: Citrate synthase
V: Citrate synthase
W: Citrate synthase
X: Citrate synthase
Y: Citrate synthase
Z: Citrate synthase
a: Citrate synthase
b: Citrate synthase
c: Citrate synthase
d: Citrate synthase
m: Citrate synthase
n: Citrate synthase
o: Citrate synthase
p: Citrate synthase
q: Citrate synthase
r: Citrate synthase
s: Citrate synthase
t: Citrate synthase
u: Citrate synthase
v: Citrate synthase
w: Citrate synthase
x: Citrate synthase
y: Citrate synthase
z: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)2,396,86754
Polymers2,396,86754
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Citrate synthase


Mass: 44386.422 Da / Num. of mol.: 54 / Mutation: H369R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
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: Second order Sierpinski triangle formed by the citrate synthase from Synechoccocus elongatus
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (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 defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17191 / Symmetry type: POINT

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