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- EMDB-44895: Cryo-EM structure of extracellular tube from Microcystis Aerugino... -

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Basic information

Entry
Database: EMDB / ID: EMD-44895
TitleCryo-EM structure of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Map datacryo-EM map of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Sample
  • Complex: pili filaments
    • Protein or peptide: pilin
Keywordsextracellular tube / filament / pili / helical symmetry / PROTEIN FIBRIL
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806SL (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPetersen HA / Ricca JG / Louda JW / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: Nat Commun / Year: 2025
Title: A family of tubular pili from harmful algal bloom forming cyanobacterium Microcystis aeruginosa.
Authors: John G Ricca / Holly A Petersen / Adam Grosvirt-Dramen / Xavier Mayali / Sarah H Naylon / Bobby G Duersch / Craig P Dufresne / Peter K Weber / Ravi R Sonani / Peter E Prevelige / Allon I ...Authors: John G Ricca / Holly A Petersen / Adam Grosvirt-Dramen / Xavier Mayali / Sarah H Naylon / Bobby G Duersch / Craig P Dufresne / Peter K Weber / Ravi R Sonani / Peter E Prevelige / Allon I Hochbaum / Vivian Merk / J W Louda / Fengbin Wang /
Abstract: Cyanobacteria are vital photosynthetic prokaryotes, but some form harmful algal blooms (cyanoHABs) that disrupt ecosystems and produce toxins. The mechanisms by which these blooms form have yet to be ...Cyanobacteria are vital photosynthetic prokaryotes, but some form harmful algal blooms (cyanoHABs) that disrupt ecosystems and produce toxins. The mechanisms by which these blooms form have yet to be fully understood, particularly the role of extracellular components. Here, we present a 2.4 Å cryo-EM structure of a pilus, termed the cyanobacterial tubular (CT) pilus, found in the cyanoHAB-forming Microcystis aeruginosa. The pilin exhibits a unique protein fold, forming a tubular pilus structure with tight, double-layer anti-parallel β-sheet interactions. We show that CT pili are essential for buoyancy by facilitating the formation of micro-colonies, which increases drag force and prevents sinking. The CT pilus surface is heavily glycosylated with ten monosaccharide modifications per pilin. Furthermore, CT pili can enrich microcystin, potentially enhancing cellular resilience, and co-localize with iron-enriched extracellular matrix components. Thus, we propose that this pilus plays an important role in the proliferation of cyanoHABs. This just discovered pilus family appears to be widely distributed across several cyanobacterial orders. Our structural and functional characterization of CT pili provide insights into cyanobacterial cell morphology, physiology, and toxin interactions, and identify potential targets for disrupting bloom formation.
History
DepositionMay 15, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44895.png

Downloads & links

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Map

FileDownload / File: emd_44895.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.27
Minimum - Maximum-0.5425083 - 18.764292000000001
Average (Standard dev.)0.112361394 (±0.8750982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap A

Fileemd_44895_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_44895_half_map_2.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pili filaments

EntireName: pili filaments
Components
  • Complex: pili filaments
    • Protein or peptide: pilin

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Supramolecule #1: pili filaments

SupramoleculeName: pili filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Microcystis aeruginosa PCC 7806SL (bacteria)

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Macromolecule #1: pilin

MacromoleculeName: pilin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Microcystis aeruginosa PCC 7806SL (bacteria)
Molecular weightTheoretical: 15.515277 KDa
SequenceString:
MKASNYQEIA KAAILAGGLA AAGVLSVGES AQAQFIGTAS QSRVSAAVTS ILTDGNAAAT NSFAVEQVLP SSDYVFSGVV AVQVSYATT ISVGVGTAGA LTPVITAAEL TAPVVVNAGT QLTVERATAD AISKAATGSR FGDVSGIVRA WSAGTSVLD

UniProtKB: Uncharacterized protein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.69 Å
Applied symmetry - Helical parameters - Δ&Phi: -14.74 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1875465
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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