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- PDB-7zl4: Cryo-EM structure of archaic chaperone-usher Csu pilus of Acineto... -

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Basic information

Entry
Database: PDB / ID: 7zl4
TitleCryo-EM structure of archaic chaperone-usher Csu pilus of Acinetobacter baumannii
ComponentsCsuA/B
KeywordsCELL ADHESION / chaperone-usher pathway / bacterial adhesion / biofilm formation / Acinetobacter baumannii / Csu pili
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsPakharukova, N. / Malmi, H. / Tuittila, M. / Paavilainen, S. / Ghosal, D. / Chang, Y.W. / Jensen, G.J. / Zavialov, A.V.
Funding support Finland, 2items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CsuA/B
B: CsuA/B
C: CsuA/B
D: CsuA/B


Theoretical massNumber of molelcules
Total (without water)64,2794
Polymers64,2794
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
CsuA/B


Mass: 16069.642 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ATCC19606_12570 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6F8TDQ5

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Csu pilus of Acinetobacter baumannii / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
2EMAN2particle selection
5RELION3.0.8CTF correction
6CTFFIND4.1.13CTF correction
9UCSF Chimera1.15model fitting
13RELION3.0.8classification
14RELION3.0.83D reconstruction
15PHENIX1.8.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -152.8 ° / Axial rise/subunit: 27.97 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 480064
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255833 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6FM5

6fm5


Pdb chain-ID: A
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 110.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0073434
ELECTRON MICROSCOPYf_angle_d1.38794695
ELECTRON MICROSCOPYf_chiral_restr0.0903573
ELECTRON MICROSCOPYf_plane_restr0.0048623
ELECTRON MICROSCOPYf_dihedral_angle_d16.40551178

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