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Yorodumi- PDB-7zl4: Cryo-EM structure of archaic chaperone-usher Csu pilus of Acineto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zl4 | |||||||||
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Title | Cryo-EM structure of archaic chaperone-usher Csu pilus of Acinetobacter baumannii | |||||||||
Components | CsuA/B | |||||||||
Keywords | CELL ADHESION / chaperone-usher pathway / bacterial adhesion / biofilm formation / Acinetobacter baumannii / Csu pili | |||||||||
Function / homology | Spore coat protein U / Spore Coat Protein U domain / Spore Coat Protein U domain / Uncharacterized protein Function and homology information | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Pakharukova, N. / Malmi, H. / Tuittila, M. / Paavilainen, S. / Ghosal, D. / Chang, Y.W. / Jensen, G.J. / Zavialov, A.V. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zl4.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zl4.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 7zl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zl4_validation.pdf.gz | 750 KB | Display | wwPDB validaton report |
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Full document | 7zl4_full_validation.pdf.gz | 749.8 KB | Display | |
Data in XML | 7zl4_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 7zl4_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/7zl4 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/7zl4 | HTTPS FTP |
-Related structure data
Related structure data | 14777MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Csu pilus of Acinetobacter baumannii / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -152.8 ° / Axial rise/subunit: 27.97 Å / Axial symmetry: D1 | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 480064 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255833 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6FM5 Pdb chain-ID: A | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.98 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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