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- EMDB-70296: Cryo-Electron Microscopy of BfpB Reveals a Type IVb Secretin Mult... -

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Basic information

Entry
Database: EMDB / ID: EMD-70296
TitleCryo-Electron Microscopy of BfpB Reveals a Type IVb Secretin Multimer Sufficient to Accommodate the Exceptionally Wide Bundle-Forming Pilus
Map data
Sample
  • Complex: BfpB
KeywordsSecretin / Type IV pili / Cryo-EM / AlphaFold / protein structure / TRANSPORT PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.72 Å
AuthorsSingh PK / Little J / Samso M / Donnenberg M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI123964-01 United States
CitationJournal: Pathogens / Year: 2025
Title: Cryo-Electron Microscopy of BfpB Reveals a Type IVb Secretin Multimer Adapted to Accommodate the Exceptionally Wide Bundle-Forming Pilus.
Authors: Janay I Little / Pradip Kumar Singh / Montserrat Samsó / Michael S Donnenberg /
Abstract: Type IV pili (T4Ps) are multifunctional surface fibers essential for bacterial motility, adhesion, and virulence, found across Gram-negative and Gram-positive bacteria and archaea. Detailed ...Type IV pili (T4Ps) are multifunctional surface fibers essential for bacterial motility, adhesion, and virulence, found across Gram-negative and Gram-positive bacteria and archaea. Detailed descriptions of T4P structural biology are allowing progress in understanding T4P biogenesis. Secretins, large outer membrane channels, are crucial for T4P extrusion in Gram-negative bacteria. Using cryo-EM and AlphaFold, we modeled the structure of BfpB, the secretin of the Bundle-Forming Pilus (BFP) of enteropathogenic . BfpB exhibits a unique 17-fold symmetry, correlating with the thicker BFP filaments, and diverging from the 12-15 subunits typical of T4P, type 2 secretion (T2S), and type 3 secretion (T3S) systems. Additionally, we identified an extended β-hairpin loop in the N3 domain, resembling features of distantly related T3SS secretins, and an N-terminal helix where a C-terminal S-domain is seen in some T2S and T3S secretins. These findings reveal evolutionary parallels and structural adaptations in secretins, highlighting the link between oligomerization and pilus structure. This work advances our understanding of T4P biogenesis, secretin evolution, and bacterial secretion systems, offering insights into pathogenic diversity and future research directions.
History
DepositionApr 23, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70296.png

Downloads & links

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Map

FileDownload / File: emd_70296.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 256 pix.
= 430.08 Å		1.68 Å/pix.
x 256 pix.
= 430.08 Å		1.68 Å/pix.
x 256 pix.
= 430.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.6831972 - 1.4764259
Average (Standard dev.)-0.012893515 (±0.055471968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70296_msk_1.map
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Half map: #2

Fileemd_70296_half_map_1.map
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Half map: #1

Fileemd_70296_half_map_2.map
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Sample components

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Entire : BfpB

EntireName: BfpB
Components
  • Complex: BfpB

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Supramolecule #1: BfpB

SupramoleculeName: BfpB / type: complex / ID: 1 / Parent: 0
Details: BfpB is a pore complex present on outer membrane of Gram negative bacteria having Type IV pili.
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1013.2 MDa

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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

Concentration0.03 mg/mL
BufferpH: 8
Details: 50 mM tris, 300 mM NaCl, pH 8.0.+ 0.02% (w/v) SB3-14
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER / Details: glow discharged for 40 second at 25 mAmp.
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified BfpB,Type IV pili secretin protein.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 9248 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsCalibrated defocus max: 5.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 54000 / Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25675
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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