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- PDB-9btq: Cryo-EM structure of extracellular tube from Microcystis Aerugino... -

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Basic information

Entry
Database: PDB / ID: 9btq
TitleCryo-EM structure of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Componentspilin
KeywordsPROTEIN FIBRIL / extracellular tube / filament / pili / helical symmetry
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806SL (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPetersen, H.A. / Ricca, J.G. / Louda, J.W. / Wang, F.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pilin


Theoretical massNumber of molelcules
Total (without water)15,5151
Polymers15,5151
Non-polymers00
Water00
1
A: pilin
x 40


Theoretical massNumber of molelcules
Total (without water)620,61140
Polymers620,61140
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation39
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 40 / Rise per n subunits: 3.648 Å / Rotation per n subunits: -14.737 °)

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Components

#1: Protein pilin


Mass: 15515.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Microcystis aeruginosa PCC 7806SL (bacteria)
References: UniProt: L7EE41
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: pili filaments / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Microcystis aeruginosa PCC 7806SL (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -14.74 ° / Axial rise/subunit: 3.69 Å / Axial symmetry: C1
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1875465 / Symmetry type: HELICAL
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00640440
ELECTRON MICROSCOPYf_angle_d1.12855440
ELECTRON MICROSCOPYf_dihedral_angle_d5.0565160
ELECTRON MICROSCOPYf_chiral_restr0.0587960
ELECTRON MICROSCOPYf_plane_restr0.0046480

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