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- EMDB-75299: Single particle reconstruction of PilU from Vibrio cholerae El To... -

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Basic information

Entry
Database: EMDB / ID: EMD-75299
TitleSingle particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 4
Map dataSingle particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 4
Sample
  • Organelle or cellular component: PilU retraction ATPase
    • Protein or peptide: PilT/PilU family type 4a pilus ATPase
KeywordsRetraction ATPase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / MOTOR PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsGuo Y / Shulka S / Klose T / Tokars V / Mondragon A / Borek D / Satchell K
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75299.png

Downloads & links

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Map

FileDownload / File: emd_75299.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 4
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 432 pix.
= 465.696 Å		1.08 Å/pix.
x 432 pix.
= 465.696 Å		1.08 Å/pix.
x 432 pix.
= 465.696 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.25989285 - 0.69882
Average (Standard dev.)-0.00021296134 (±0.012208246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 465.69598 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Density modified

Fileemd_75299_additional_1.map
AnnotationDensity modified
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: Half Map B

Fileemd_75299_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_75299_half_map_2.map
AnnotationHalf Map A
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 : PilU retraction ATPase

EntireName: PilU retraction ATPase
Components
  • Organelle or cellular component: PilU retraction ATPase
    • Protein or peptide: PilT/PilU family type 4a pilus ATPase

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Supramolecule #1: PilU retraction ATPase

SupramoleculeName: PilU retraction ATPase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: PilT/PilU family type 4a pilus ATPase

MacromoleculeName: PilT/PilU family type 4a pilus ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 42.949852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGGSGGHHH HHHAGGAGGE LNQYLDGMLT HKASDLYITV GAPILYRVDG ELRAQGEALS VADVTALLHA MMDDARQAEF KQTREANFA VVRDSGRFRV SAFFQRELPG AVIRRIETRI PTFEELKLPE VLQNLAIAKR GLVLVVGATG SGKSTTMAAM T GYRNQHRT ...String:
MAGGSGGHHH HHHAGGAGGE LNQYLDGMLT HKASDLYITV GAPILYRVDG ELRAQGEALS VADVTALLHA MMDDARQAEF KQTREANFA VVRDSGRFRV SAFFQRELPG AVIRRIETRI PTFEELKLPE VLQNLAIAKR GLVLVVGATG SGKSTTMAAM T GYRNQHRT GHILTVEDPI EFVHEHKRCI VTQREVGLDT ESYEVALKNS LRQAPDMILI GEIRSRETME YAMTFAETGH LC MATLHAN NANQALERIL HLVPKEQREQ FLLDLSLNLK GVIAQQLLRD KNGKGRHGVF EVLLNSPRIA DLIRRGELHE LKA TMARSQ EVGMQTFDQA LYQLVVDDKI SEQDALHSAD SANDLRLMLK TKRGDDYGSG SLQNVKIDME

UniProtKB: PilT/PilU family type 4a pilus ATPase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 128808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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