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- EMDB-73615: Sub-tomogram averaged structure of the non-piliated Tad machine i... -

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Basic information

Entry
Database: EMDB / ID: EMD-73615
TitleSub-tomogram averaged structure of the non-piliated Tad machine in Caulobacter crescentus
Map dataFull main map of the non piliated Tad machine in Caulobacter crescentus.
Sample
  • Cell: Caulobacter crescentus bNY30a
KeywordsTad Pilus / Caulobacter crescentus / Surface Sensing / Type IV Pilus / CELL ADHESION
Biological speciesCaulobacter vibrioides (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 42.02 Å
AuthorsIarocci J / Williston RF / Guo S
Funding support Canada, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2024-04631 Canada
Fonds de Recherche du Quebec - Sante (FRQS)359456 & 376506 Canada
CitationJournal: To Be Published
Title: In situ Architecture of the Tad Pilus Machine in Caulobacter crescentus
Authors: Iarocci J / Whitfield GB / Williston RF / Brun YV / Guo S
History
DepositionOct 27, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73615.png

Downloads & links

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Map

FileDownload / File: emd_73615.map.gz / Format: CCP4 / Size: 6.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull main map of the non piliated Tad machine in Caulobacter crescentus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.48 Å/pix.
x 118 pix.
= 1000.64 Å		8.48 Å/pix.
x 118 pix.
= 1000.64 Å		8.48 Å/pix.
x 118 pix.
= 1000.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.469
Minimum - Maximum-2.4331398 - 1.4010197
Average (Standard dev.)0.000000002485665 (±0.1360988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions118118118
Spacing118118118
CellA=B=C: 1000.63995 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Odd half map of the non piliated Tad...

Fileemd_73615_half_map_1.map
AnnotationOdd half map of the non piliated Tad machine in Caulobacter crescentus.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Even half map of the non piliated Tad...

Fileemd_73615_half_map_2.map
AnnotationEven half map of the non piliated Tad machine in Caulobacter crescentus.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Caulobacter crescentus bNY30a

EntireName: Caulobacter crescentus bNY30a
Components
  • Cell: Caulobacter crescentus bNY30a

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Supramolecule #1: Caulobacter crescentus bNY30a

SupramoleculeName: Caulobacter crescentus bNY30a / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: bNY30a

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Details: Manual Plunge Freezer.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -6.5 µm / Nominal defocus min: -4.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 42.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: I3 / Number subtomograms used: 842
ExtractionNumber tomograms: 64 / Number images used: 842 / Software - Name: I3
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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