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- PDB-10nb: Single particle reconstruction of PilU from Vibrio cholerae El To... -

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Basic information

Entry
Database: PDB / ID: 10nb
TitleSingle particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 4
ComponentsPilT/PilU family type 4a pilus ATPase
KeywordsMOTOR PROTEIN / Retraction ATPase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologyPilus retraction protein PilT/PilU / : / Type II/IV secretion system protein / Type II/IV secretion system protein / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / PilT/PilU family type 4a pilus ATPase
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsGuo, Y. / Shulka, S. / Klose, T. / Tokars, V. / Mondragon, A. / Borek, D. / Satchell, K. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci / Year: 2026
Title: Analysis of the heterogenous structural states of the hexameric ATPase PilU of the type IV pili from Vibrio cholerae.
Authors: Yirui Guo / Shantanu Shukla / George Minasov / Nicole L Inniss / Thomas Klose / Valerie L Tokars / Alfonso Mondragón / Zbyszek Otwinowski / Dominika Borek / Karla J F Satchell /
Abstract: Type IV pili (T4P) mediate surface motility, host interactions, and DNA uptake through cycles of extension and retraction. While the primary retraction ATPase PilT has been extensively characterized, ...Type IV pili (T4P) mediate surface motility, host interactions, and DNA uptake through cycles of extension and retraction. While the primary retraction ATPase PilT has been extensively characterized, its homolog PilU remains less well understood despite being demonstrated as a PilT-dependent retraction ATPase. Here, we determined six PilU structures by cryo-electron microscopy and x-ray crystallography. The structures reveal a homohexameric assembly stabilized by interactions between the C-terminal catalytic domain of one subunit and the N-terminal PAS-like domain of a neighboring subunit. PilU adopts multiple conformational states, exhibiting different combinations of open and closed interfaces even in the absence of nucleotide. Comparison with PilT highlights structural features that likely underlie PilU's weak ATPase activity and its dependence on PilT for function. Together, these findings provide a structural framework for understanding PilU's role within the T4P retraction machinery.
History
DepositionJan 28, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PilT/PilU family type 4a pilus ATPase
B: PilT/PilU family type 4a pilus ATPase
C: PilT/PilU family type 4a pilus ATPase
D: PilT/PilU family type 4a pilus ATPase
E: PilT/PilU family type 4a pilus ATPase
F: PilT/PilU family type 4a pilus ATPase


Theoretical massNumber of molelcules
Total (without water)257,6996
Polymers257,6996
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
PilT/PilU family type 4a pilus ATPase / Type IV pili twitching motility protein PilT


Mass: 42949.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: BC353_02195, D6U24_12630, FLM02_06300, KIN13_15985 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085SZ25
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PilU retraction ATPase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.3
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128808 / Symmetry type: POINT

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