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- EMDB-14777: Cryo-EM structure of archaic chaperone-usher Csu pilus of Acineto... -

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Basic information

Entry
Database: EMDB / ID: EMD-14777
TitleCryo-EM structure of archaic chaperone-usher Csu pilus of Acinetobacter baumannii
Map data
Sample
  • Organelle or cellular component: Csu pilus of Acinetobacter baumannii
    • Protein or peptide: CsuA/B
Function / homologySpore coat protein U / Spore Coat Protein U domain / Spore Coat Protein U domain / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsPakharukova N / Malmi H / Tuittila M / Paavilainen S / Ghosal D / Chang YW / Jensen GJ / Zavialov AV
Funding support Finland, 2 items
OrganizationGrant numberCountry
Academy of Finland273075 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Nature / Year: 2022
Title: Archaic chaperone-usher pili self-secrete into superelastic zigzag springs.
Authors: Natalia Pakharukova / Henri Malmi / Minna Tuittila / Tobias Dahlberg / Debnath Ghosal / Yi-Wei Chang / Si Lhyam Myint / Sari Paavilainen / Stefan David Knight / Urpo Lamminmäki / Bernt Eric ...Authors: Natalia Pakharukova / Henri Malmi / Minna Tuittila / Tobias Dahlberg / Debnath Ghosal / Yi-Wei Chang / Si Lhyam Myint / Sari Paavilainen / Stefan David Knight / Urpo Lamminmäki / Bernt Eric Uhlin / Magnus Andersson / Grant Jensen / Anton V Zavialov /
Abstract: Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria. Archaic chaperone-usher ...Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria. Archaic chaperone-usher pathway pili, the most diverse and widespread chaperone-usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens. However, their architecture and assembly-secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii-a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed for the first time, to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.
History
DepositionApr 13, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14777.png

Downloads & links

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Map

FileDownload / File: emd_14777.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 128 pix.
= 165.747 Å		1.29 Å/pix.
x 128 pix.
= 165.747 Å		1.29 Å/pix.
x 128 pix.
= 165.747 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2949 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.26733786 - 0.48615435
Average (Standard dev.)-6.5067165e-05 (±0.013017774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 165.7472 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 2

Fileemd_14777_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_14777_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Csu pilus of Acinetobacter baumannii

EntireName: Csu pilus of Acinetobacter baumannii
Components
  • Organelle or cellular component: Csu pilus of Acinetobacter baumannii
    • Protein or peptide: CsuA/B

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Supramolecule #1: Csu pilus of Acinetobacter baumannii

SupramoleculeName: Csu pilus of Acinetobacter baumannii / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: CsuA/B

MacromoleculeName: CsuA/B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 16.069642 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AVTGQVDVKL NISTGCTVGG SQTEGNMNKF GTLNFGKTSG TWNNVLTAEV ASAATGGNIS VTCDGTDPVD FTVAIDGGER TDRTLKNTA SADVVAYNVY RDAARTNLYV VNQPQQFTTV SGQATAVPIF GAIAPNTGTP KAQGDYKDTL LVTVNF

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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: 7.4
GridModel: Quantifoil / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 480064 / Software - Name: EMAN2
CTF correctionSoftware: (Name: RELION (ver. 3.0.8), CTFFIND (ver. 4.1.13))
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6fm5


Details: Crystal structure of self-complemented CsuA/B major subunit was fitted into the density of the polymer
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.97 Å
Applied symmetry - Helical parameters - Δ&Phi: -152.8 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 255833
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fm5


Chain - Chain ID: A
RefinementSpace: REAL
Output model

PDB-7zl4:
Cryo-EM structure of archaic chaperone-usher Csu pilus of Acinetobacter baumannii

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