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- EMDB-16004: Structure of hexameric subcomplexes (Truncation Delta2-6) of the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16004
TitleStructure of hexameric subcomplexes (Truncation Delta2-6) of the fractal citrate synthase from Synechococcus elongatus PCC7942
Map data
Sample
  • Complex: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942
    • Protein or peptide: Citrate synthase
KeywordsFractal complex / TRANSFERASE
Function / homology
Function and homology information


citrate synthase activity / tricarboxylic acid cycle / cytoplasm
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: 3.06 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: To Be Published
Title: Evolution of a protein Sierpinski fractal
Authors: Sendker LF / Lo YK / Heimerl T / Bohn S / Pfister P / Mais N / Sadowska W / Peterson L / Benesch JLP / Marklund E / Bange G / Erb TJ / Schuller JM / Hochberg GKA
History
DepositionOct 21, 2022-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16004.png

Downloads & links

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Map

FileDownload / File: emd_16004.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.16013925 - 0.2589481
Average (Standard dev.)0.00000893993 (±0.0060111005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16004_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_16004_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Truncated (Delta 2-6) variant of the citrate synthase from Synech...

EntireName: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942
Components
  • Complex: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942
    • Protein or peptide: Citrate synthase

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Supramolecule #1: Truncated (Delta 2-6) variant of the citrate synthase from Synech...

SupramoleculeName: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942
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: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / FACHB-805
Molecular weightTheoretical: 43.879867 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFRPGLEGVP ATLSSISFVD GQRGVLEYRG ISIEQLAQQS SFLETAYLLI WGHLPTQQEL TEFEHEIRYH RRIKFRIRDM MKCFPDSGH PMDALQASAA ALGLFYSRRA LDDPEYIRAA VVRLLAKIPT MVAAFQLIRK GNDPIQPRDE LDYAANFLYM L TEREPDPV ...String:
MFRPGLEGVP ATLSSISFVD GQRGVLEYRG ISIEQLAQQS SFLETAYLLI WGHLPTQQEL TEFEHEIRYH RRIKFRIRDM MKCFPDSGH PMDALQASAA ALGLFYSRRA LDDPEYIRAA VVRLLAKIPT MVAAFQLIRK GNDPIQPRDE LDYAANFLYM L TEREPDPV AARIFDICLT LHAEHTINAS TFSAMVTAST LTDPYAVVAS AVGTLAGPLH GGANEEVLDM LEAIGSVENV EP YLDHCIA TKTRIMGFGH RVYKVKDPRA VILQNLAEQL FDIFGHDPYY EIAVAVEKAA AERLSHKGIY PNVDFYSGLV YRK LGIPSD LFTPVFAIAR VAGWLAHWKE QLNENRIFRP TQIYTGSHNL DYTPIADRDL AIESDLEHHH HHH

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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 774026
FSC plot (resolution estimation)

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