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- PDB-8uhf: Cryo-EM of Vibrio cholerae toxin co-regulated pilus - asymmetric ... -

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Basic information

Entry
Database: PDB / ID: 8uhf
TitleCryo-EM of Vibrio cholerae toxin co-regulated pilus - asymmetric reconstruction
ComponentsToxin co-regulated pilin
KeywordsCELL ADHESION / Toxin / Cholera / Type IV pilus
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 co-regulated pilin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSonani, R.R. / Kundra, S. / Craig, L. / Egelman, E.H.
Funding support United States, 1items
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
DepositionOct 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 6, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 6, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Category: em_admin / pdbx_database_related / Item: _em_admin.last_update
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / pdbx_database_related / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin co-regulated pilin
B: Toxin co-regulated pilin
C: Toxin co-regulated pilin
D: Toxin co-regulated pilin
E: Toxin co-regulated pilin
F: Toxin co-regulated pilin
G: Toxin co-regulated pilin
H: Toxin co-regulated pilin
I: Toxin co-regulated pilin


Theoretical massNumber of molelcules
Total (without water)182,4779
Polymers182,4779
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Filament visible in EM microgrphs
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Toxin co-regulated pilin


Mass: 20275.205 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: Q93TT5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Toxin co-regulated pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio cholerae (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 115603 / Details: Model-to-map FSC, threshold 0.5 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212542
ELECTRON MICROSCOPYf_angle_d0.49817011
ELECTRON MICROSCOPYf_dihedral_angle_d2.3157577
ELECTRON MICROSCOPYf_chiral_restr0.0382143
ELECTRON MICROSCOPYf_plane_restr0.0032179

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