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- EMDB-19250: Pseudoatomic model of a second-order Sierpinski triangle formed b... -

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Basic information

Entry
Database: EMDB / ID: EMD-19250
TitlePseudoatomic model of a second-order Sierpinski triangle formed by the citrate synthase from Synechococcus elongatus
Map data
Sample
  • Complex: Second order Sierpinski triangle formed by the citrate synthase from Synechoccocus elongatus
    • Protein or peptide: Citrate synthase
KeywordsFractal complex / TRANSFERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.91 Å
AuthorsLo YK / Bohn S / Sendker FL / Schuller JM / Hochberg G
Funding support Germany, European Union, 3 items
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, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19250.png

Downloads & links

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Map

FileDownload / File: emd_19250.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 600 pix.
= 948. Å		1.58 Å/pix.
x 600 pix.
= 948. Å		1.58 Å/pix.
x 600 pix.
= 948. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.3332858 - 0.91790307
Average (Standard dev.)0.00051776797 (±0.026348403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 948.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19250_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19250_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Second order Sierpinski triangle formed by the citrate synthase f...

EntireName: Second order Sierpinski triangle formed by the citrate synthase from Synechoccocus elongatus
Components
  • Complex: Second order Sierpinski triangle formed by the citrate synthase from Synechoccocus elongatus
    • Protein or peptide: Citrate synthase

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Supramolecule #1: Second order Sierpinski triangle formed by the citrate synthase f...

SupramoleculeName: Second order Sierpinski triangle formed by the citrate synthase from Synechoccocus elongatus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)

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Macromolecule #1: Citrate synthase

MacromoleculeName: Citrate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 54 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 44.386422 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTAVSEFRPG LEGVPATLSS ISFVDGQRGV LEYRGISIEQ LAQQSSFLET AYLLIWGHLP TQQELTEFEH EIRYHRRIKF RIRDMMKCF PDSGHPMDAL QASAAALGLF YSRRALDDPE YIRAAVVRLL AKIPTMVAAF QLIRKGNDPI QPRDELDYAA N FLYMLTER ...String:
MTAVSEFRPG LEGVPATLSS ISFVDGQRGV LEYRGISIEQ LAQQSSFLET AYLLIWGHLP TQQELTEFEH EIRYHRRIKF RIRDMMKCF PDSGHPMDAL QASAAALGLF YSRRALDDPE YIRAAVVRLL AKIPTMVAAF QLIRKGNDPI QPRDELDYAA N FLYMLTER EPDPVAARIF DICLTLHAEH TINASTFSAM VTASTLTDPY AVVASAVGTL AGPLHGGANE EVLDMLEAIG SV ENVEPYL DHCIATKTRI MGFGHRVYKV KDPRAVILQN LAEQLFDIFG HDPYYEIAVA VEKAAAERLS HKGIYPNVDF YSG LVYRKL GIPSDLFTPV FAIARVAGWL AHWKEQLNEN RIFRPTQIYT GSRNLDYTPI ADRDLAIESD LEHHHHHH

UniProtKB: Citrate synthase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17191
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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