[English] 日本語
Yorodumi
- EMDB-73615: Sub-tomogram averaged structure of the non-piliated Tad machine i... -

+
Open data


ID or keywords:

Loading...

-
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: mBio / Year: 2026
Title: architecture of the Tad pilus machine in .
Authors: James Iarocci / Gregory B Whitfield / Ryu F Williston / Michael R Wozny / Kaustuv Basu / John F Presley / Courtney K Ellison / Yves V Brun / Shuaiqi Guo /
Abstract: The tight adherence (Tad) pilus is a broadly distributed and evolutionarily distinct subclass of type IV pili that mediate cell adhesion, biofilm formation, predation, and surface sensing in many ...The tight adherence (Tad) pilus is a broadly distributed and evolutionarily distinct subclass of type IV pili that mediate cell adhesion, biofilm formation, predation, and surface sensing in many bacteria, including , , , and . Tad pili undergo cycles of extension and retraction powered by a cell-envelope-embedded nanomachine. Despite their biological importance, the architecture and assembly mechanism of the Tad pilus system remain poorly understood. Although cryo-electron tomography (cryo-ET) has elucidated the architectures of other type IV pilus systems, no intact Tad machine structure has previously been reported. Here, we use cryo-ET and subtomogram averaging to resolve the architecture of the Tad pilus within the bacterial cell envelope. A three-dimensional classification further reveals multiple assembly intermediates, and integrative modeling incorporating AlphaFold3 predictions helps define the spatial arrangement of all core components. The resulting structural framework gives insight into the stepwise assembly process of the Tad pilus machine. Altogether, our results provide an architectural model of the Tad pilus machine, establishing a foundation for understanding homologous systems across a broad range of bacteria.
IMPORTANCE: Investigating the Tad pilus nanomachine in a genetically tractable, non-pathogenic organism like provides a powerful model for elucidating the architecture and functional dynamics of ...IMPORTANCE: Investigating the Tad pilus nanomachine in a genetically tractable, non-pathogenic organism like provides a powerful model for elucidating the architecture and functional dynamics of this widespread system. Insights gained from studying the Tad machinery can improve our understanding of related Tad pilus systems in pathogenic bacteria such as , where Tad pili are a key determinant of biofilm formation and chronic infection. Additionally, the remarkable functional diversity of Tad systems, ranging from surface sensing in to bacterial predation in , highlights their broad biological relevance. By revealing the architecture of the Tad pilus biosynthetic machinery, this study advances our understanding of a major class of bacterial nanomachines and may thus provide structural insights that could inform the development of new therapeutic strategies targeting pilus-mediated virulence.
History
DepositionOct 27, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73615.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

-
Entire : Caulobacter crescentus bNY30a

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

-
Supramolecule #1: Caulobacter crescentus bNY30a

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more