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- EMDB-18593: CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus -

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Basic information

Entry
Database: EMDB / ID: EMD-18593
TitleCryoEM structure of the type IV pilin PilA5 from Thermus thermophilus
Map data
Sample
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: Type IV narrow pilus major component PilA5
  • Ligand: MAGNESIUM ION
KeywordsType IV pilin glycosylation / twitching motility / PROTEIN FIBRIL
Function / homologyProkaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / cell outer membrane / periplasmic space / plasma membrane / Type IV narrow pilus major component PilA5
Function and homology information
Biological speciesThermus thermophilus HB27 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsGold VAM / Neuhaus A / Gaines M / Isupov M / McLaren M
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
DepositionOct 4, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18593.png

Downloads & links

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Map

FileDownload / File: emd_18593.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.082781 - 0.9999999
Average (Standard dev.)0.15038465 (±0.016491134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 536.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18593_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18593_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Thermus thermophilus wide pilus

EntireName: Thermus thermophilus wide pilus
Components
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: Type IV narrow pilus major component PilA5
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Thermus thermophilus wide pilus

SupramoleculeName: Thermus thermophilus wide pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)

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Macromolecule #1: Type IV narrow pilus major component PilA5

MacromoleculeName: Type IV narrow pilus major component PilA5 / type: protein_or_peptide / ID: 1 / Number of copies: 31 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Molecular weightTheoretical: 11.441797 KDa
SequenceString:
FTLIELAIVI VIIGILVAIA VPRFVDLTDQ ANQANVDATA AAVRSAYAIA TVQAKGIPTC DQVFANLEGG STSGSTWTSS DNSTTVSCN ASADTFTISR GGKTRTLNLT VN

UniProtKB: Type IV narrow pilus major component PilA5

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 31 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 1-40 / Number real images: 2455 / Average electron dose: 47.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.25 Å
Applied symmetry - Helical parameters - Δ&Phi: 84.0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 475441
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2763060 / Software - Name: cryoSPARC
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8qqj:
CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus

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