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- EMDB-18588: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus -

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Basic information

Entry
Database: EMDB / ID: EMD-18588
TitleCryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
Map data
Sample
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: PilA
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
KeywordsType IV pilin glycosylation / twitching motility / PROTEIN FIBRIL
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / periplasmic space
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesThermus thermophilus HB27 (bacteria) / Thermus thermophilus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 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_18588.png

Downloads & links

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Map

FileDownload / File: emd_18588.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 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: 0.035
Minimum - Maximum-0.078599975 - 0.34300625
Average (Standard dev.)0.00023322304 (±0.0077365907)
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_18588_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_18588_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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: PilA
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose

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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: PilA

MacromoleculeName: PilA / type: protein_or_peptide / ID: 1 / Number of copies: 45 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 13.251123 KDa
SequenceString:
FTLIELLIVI AIIAILAAVL IPNLLAARKR ANDTVVTAYL NDAVKFQEMY QIDNNSYTSN QAALISLGLK STPANVTFSI VSASANSYC MIAGHSGGTV WFAATPDKGV YKTNTAVTSS QPESCP

UniProtKB: PilA

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Macromolecule #4: 2-acetamido-2-deoxy-alpha-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-galactopyranose / type: ligand / ID: 4 / Number of copies: 45 / Formula: A2G
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 1-40 / 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: 9.242 Å
Applied symmetry - Helical parameters - Δ&Phi: 92.36 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 654248
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8qqd:
CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus

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