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- EMDB-41968: Cryo-EM of Vibrio cholera toxin co-regulated pilus (TCP) -

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Basic information

Entry
Database: EMDB / ID: EMD-41968
TitleCryo-EM of Vibrio cholera toxin co-regulated pilus (TCP)
Map data
Sample
  • Complex: Toxin co-regulated pilus
    • Protein or peptide: Toxin coregulated pilin
KeywordsToxin / Cholera / Type IV pilus / CELL ADHESION
Function / homology
Function and homology information


extracellular organelle / pilus / membrane
Similarity search - Function
Toxin-coregulated pilus subunit TcpA / Toxin-coregulated pilus subunit TcpA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Toxin coregulated pilin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsSonani RR / Kundra S / Craig L / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Tad and toxin-coregulated pilus structures reveal unexpected diversity in bacterial type IV pili.
Authors: Ravi R Sonani / Juan Carlos Sanchez / Joseph K Baumgardt / Shivani Kundra / Elizabeth R Wright / Lisa Craig / Edward H Egelman /
Abstract: Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal ...Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P.
History
DepositionSep 14, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41968.png

Downloads & links

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Map

FileDownload / File: emd_41968.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29197547 - 0.49051952
Average (Standard dev.)0.0023427724 (±0.02256597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpned map by DeepEMhancer

Fileemd_41968_additional_1.map
AnnotationSharpned map by DeepEMhancer
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_41968_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_41968_half_map_2.map
Projections & Slices
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Sample components

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Entire : Toxin co-regulated pilus

EntireName: Toxin co-regulated pilus
Components
  • Complex: Toxin co-regulated pilus
    • Protein or peptide: Toxin coregulated pilin

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Supramolecule #1: Toxin co-regulated pilus

SupramoleculeName: Toxin co-regulated pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: Toxin coregulated pilin

MacromoleculeName: Toxin coregulated pilin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 20.342275 KDa
SequenceString: MTLLEVIIVL GIMGVVSAGV VTLAQRAIDS QIMTKAAQSL NSIQVALTQT YRGLGNYPAT ADATAASKLT SGLVSLGKIS SDEAKNPFN GTNMNIFSFP RNAAANKAFA ISVDGLTQAQ CKTLITSVGD MFPYIAIKAG GAVALADLGD FENSAAAAET G VGVIKSIA ...String:
MTLLEVIIVL GIMGVVSAGV VTLAQRAIDS QIMTKAAQSL NSIQVALTQT YRGLGNYPAT ADATAASKLT SGLVSLGKIS SDEAKNPFN GTNMNIFSFP RNAAANKAFA ISVDGLTQAQ CKTLITSVGD MFPYIAIKAG GAVALADLGD FENSAAAAET G VGVIKSIA PASKNLDLTN ITHVEKLCKG TAPFGVAFGN S

UniProtKB: Toxin coregulated pilin

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.306 Å
Applied symmetry - Helical parameters - Δ&Phi: 96.98 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33045
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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