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- EMDB-18852: Structure of the BeeR filament -

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Basic information

Entry
Database: EMDB / ID: EMD-18852
TitleStructure of the BeeR filament
Map dataStructure of the BeeR filament
Sample
  • Complex: BeeR filament
    • Protein or peptide: Actin/actin family protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsBacterial cytoskeleton / actin homologue / STRUCTURAL PROTEIN
Function / homology: / MreB/Mbl protein / Actin family / Actin / ATPase, nucleotide binding domain / ATP binding / cytoplasm / Actin/actin family protein
Function and homology information
Biological speciesOpitutus terrae (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBergeron JRC / Kollman JM
Funding support United Kingdom, France, United States, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R009759/2 United Kingdom
Human Frontier Science Program (HFSP)RGY0080/2021 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35149542 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: A family of bacterial actin homologs forms a three-stranded tubular structure.
Authors: Julien R C Bergeron / Shamar L M Lale-Farjat / Hanna M Lewicka / Chloe Parry / Justin M Kollman /
Abstract: The cytoskeleton is crucial for cell organization and movement. In Eukaryotes, it largely consists of the protein actin, that forms a double-stranded linear filamentous structure in the presence of ...The cytoskeleton is crucial for cell organization and movement. In Eukaryotes, it largely consists of the protein actin, that forms a double-stranded linear filamentous structure in the presence of ATP and disassemble upon ATP hydrolysis. Bacteria also possess actin homologs, that drive fundamental cellular processes, including cell division, shape maintenance, and DNA segregation. Like eukaryotic actin, bacterial actins assemble into dynamic polymers upon ATP binding, however variation in interactions between strands gives rise to striking diversity of filament architectures. Here, we report a family of bacterial actins of unknown function, conserved among the phylum, which assembles into a unique tubular structure in the presence of ATP. A cryo-EM structure of the filaments reveals that it consists of three strands, unlike other described bacterial actin structures. This architecture provides further insights into the organization of actin-like filaments and has implications for understanding the diversity and evolution of the bacterial cytoskeleton.
History
DepositionNov 7, 2023-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18852.png

Downloads & links

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Map

FileDownload / File: emd_18852.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the BeeR filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.129
Minimum - Maximum-0.7491335 - 1.1607919
Average (Standard dev.)0.0012009754 (±0.040681712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18852_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_18852_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 : BeeR filament

EntireName: BeeR filament
Components
  • Complex: BeeR filament
    • Protein or peptide: Actin/actin family protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: BeeR filament

SupramoleculeName: BeeR filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Opitutus terrae (bacteria)

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Macromolecule #1: Actin/actin family protein

MacromoleculeName: Actin/actin family protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Opitutus terrae (bacteria)
Molecular weightTheoretical: 41.104875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIPASTEKPV PSAAIPANAP NVAVSKPAAP GTRTKTVLVG FDFGTNKSCV LAGTAGATDI AISKIVPTVV GYVKEGIVDG IVAGNRSVL FGDDALQNRL HARLVAPMEH GVIAHPDAAR DFVQHLRSLA DPSGQAEIRA VVGVPANATE QAREDVRRCA F GIFDRILL ...String:
MIPASTEKPV PSAAIPANAP NVAVSKPAAP GTRTKTVLVG FDFGTNKSCV LAGTAGATDI AISKIVPTVV GYVKEGIVDG IVAGNRSVL FGDDALQNRL HARLVAPMEH GVIAHPDAAR DFVQHLRSLA DPSGQAEIRA VVGVPANATE QAREDVRRCA F GIFDRILL IPEPFLAALG YRDDARLGQS NYIDPVVNSL FIDIGGGTSD ICLVQGYFPG PDDQISIPFA GDAIDQLLQE EL NRTYPNN GLSLHKVREI KEAHGYVGPS RKPLDVKVVI GGKAHTLELG DTLARACNAL IDKIYPALTT LIQRASSDSV VTL LQNIII TGGGSQIKGI DTLLQKKLTE DGFESPKVRL AGHDYKRYVA LGALKAARAA RENQWQVLLG

UniProtKB: Actin/actin family protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 549 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 17.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 126.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 882189
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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