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- EMDB-51272: Low Resolution reconstruction of PilQ from filamentous Cyanobacteria -

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Basic information

Entry
Database: EMDB / ID: EMD-51272
TitleLow Resolution reconstruction of PilQ from filamentous Cyanobacteria
Map data
Sample
  • Complex: PilQ double complex
KeywordsProtein Secretion Carbohydrate Secretion Motility Cyanobacteria / MEMBRANE PROTEIN
Biological speciesArthrospira platensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsSo JMT / Hoiczyk E
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Secretins of type-two secretion systems are necessary for exopolymeric slime secretion in cyanobacteria and myxobacteria.
Authors: David M Zuckerman / Jeffery Man To So / Egbert Hoiczyk /
Abstract: Cyanobacteria and myxobacteria display gliding motility associated with the secretion of an exopolymeric slime through nozzle-like structures. Here, we use biochemical and structural assays to show ...Cyanobacteria and myxobacteria display gliding motility associated with the secretion of an exopolymeric slime through nozzle-like structures. Here, we use biochemical and structural assays to show that these nozzles are composed of secretins of the PilQ/GspD family, which are known to form outer membrane gates in type-two secretion systems (T2SSs) and other bacterial protein secretion systems. We show that gspD is an essential gene in Myxococcus xanthus, and its downregulation by conditional knockdown renders this bacterium defective in both slime secretion and gliding motility. In cyanobacteria, available data suggest that the exopolymeric slime is a polysaccharide, although the precise nature of the slime in myxobacteria remains unclear. Our results, therefore, indicate that secretins may be required for the secretion of non-proteinaceous polymers in certain bacteria.
History
DepositionAug 5, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51272.png

Downloads & links

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Map

FileDownload / File: emd_51272.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 350 pix.
= 581. Å		1.66 Å/pix.
x 350 pix.
= 581. Å		1.66 Å/pix.
x 350 pix.
= 581. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1121262 - 0.92050135
Average (Standard dev.)0.002006425 (±0.0642402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 581.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51272_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51272_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PilQ double complex

EntireName: PilQ double complex
Components
  • Complex: PilQ double complex

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Supramolecule #1: PilQ double complex

SupramoleculeName: PilQ double complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arthrospira platensis (bacteria)

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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

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (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: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 1505
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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