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- EMDB-56471: Structure of the type IV pilus machinery from Thermus thermophilu... -

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Basic information

Entry
Database: EMDB / ID: EMD-56471
TitleStructure of the type IV pilus machinery from Thermus thermophilus in the closed state (C6 symmetry)
Map data
Sample
  • Complex: Structure of the type IV pilus machinery from Thermus thermophilus in the open state (C13 symmetry)
KeywordsType IV pilus / Thermus / Bacterial motility / STRUCTURAL PROTEIN
Biological speciesThermus thermophilus HB27 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 140.0 Å
AuthorsMcLaren MJ / Neuhaus A / Gold VAM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R008639/1 United Kingdom
CitationJournal: Commun Biol / Year: 2026
Title: Structural insights into the Thermus thermophilus type IV pilus machinery assembling two distinct pili.
Authors: Alexander Neuhaus / Mathew McLaren / Michail N Isupov / Matthew Gaines / Emma Buzzard / Mateusz Sikora / Cyril Hanus / Bertram Daum / Beate Averhoff / Vicki A M Gold /
Abstract: Type IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus ...Type IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus HB27 produces two different type IV pili, each exhibiting distinct structural and functional properties. Here, we combine cryo-electron tomography, mutagenesis, and AlphaFold predictions to generate hypothetical in situ models of the T. thermophilus type IV pilus assembly machinery. Using single-particle cryo-electron microscopy, we determine structures of both filament types, enabling modelling of their surface glycans. Molecular dynamics simulations further reveal the flexibility of these glycans on extrusion. Integration of the filament structures with our hypothetical model of the assembly machinery offers a framework for further dissecting T4P architecture and biogenesis.
History
DepositionJan 22, 2026-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56471.png

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Map

FileDownload / File: emd_56471.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
8.4 Å/pix.
x 150 pix.
= 1260. Å		8.4 Å/pix.
x 150 pix.
= 1260. Å		8.4 Å/pix.
x 150 pix.
= 1260. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 8.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.585
Minimum - Maximum0.0042071342 - 0.9811168
Average (Standard dev.)0.5229674 (±0.038302705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 1260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56471_half_map_1.map
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Half map: #1

Fileemd_56471_half_map_2.map
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Sample components

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Entire : Structure of the type IV pilus machinery from Thermus thermophilu...

EntireName: Structure of the type IV pilus machinery from Thermus thermophilus in the open state (C13 symmetry)
Components
  • Complex: Structure of the type IV pilus machinery from Thermus thermophilus in the open state (C13 symmetry)

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Supramolecule #1: Structure of the type IV pilus machinery from Thermus thermophilu...

SupramoleculeName: Structure of the type IV pilus machinery from Thermus thermophilus in the open state (C13 symmetry)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.97 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 140.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: PEET (ver. 1.17.0), RELION (ver. 4.0.1)) / Number subtomograms used: 33
ExtractionNumber tomograms: 32 / Number images used: 33 / Software - Name: PEET (ver. 1.17.0)
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model

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