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Yorodumi- PDB-6y7s: 2.85 A cryo-EM structure of the in vivo assembled type 1 pilus rod -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y7s | |||||||||
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Title | 2.85 A cryo-EM structure of the in vivo assembled type 1 pilus rod | |||||||||
Components | Type-1 fimbrial protein, A chain | |||||||||
Keywords | STRUCTURAL PROTEIN / FimA / pilus / monomer / subunit / pili / main structural subunit / high resolution / cryo-EM / helical processing / RELION / Chaperone-usher pilus | |||||||||
Function / homology | Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
Authors | Zyla, D. / Hospenthal, M. / Waksman, G. / Glockshuber, R. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili. Authors: Dawid S Zyla / Thomas Wiegand / Paul Bachmann / Rafal Zdanowicz / Christoph Giese / Beat H Meier / Gabriel Waksman / Manuela K Hospenthal / Rudi Glockshuber / Abstract: Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of ...Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6y7s.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y7s.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 6y7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y7s_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6y7s_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6y7s_validation.xml.gz | 38 KB | Display | |
Data in CIF | 6y7s_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/6y7s ftp://data.pdbj.org/pub/pdb/validation_reports/y7/6y7s | HTTPS FTP |
-Related structure data
Related structure data | 10721MC 8psvC 8ptuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 18121.074 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimA, pilA, b4314, JW4277 Production host: Escherichia coli str. K-12 substr. W3110 (bacteria) References: UniProt: P04128 |
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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: Type 1 pilus rod / Type: COMPLEX Details: Type 1 pili recombinantly expressed, assembled in vivo and subsequently purified from the E. coli cell surface. Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 20.3 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli str. K-12 substr. W3110 (bacteria) |
Buffer solution | pH: 7 / Details: in ddH2O. |
Specimen | Conc.: 1.58 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 277 K Details: 3 ul sample, 30 s wait time, 0.5 s drain time, 6 s blotting |
-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: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 50.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3469 |
Image scans | Movie frames/image: 40 |
Reflection | Biso Wilson estimate: 41.26 Å2 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 115.001 ° / Axial rise/subunit: 7.85334 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 516000 Details: Autopicking based on the 2D classes from manually chosen filaments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40805 / Algorithm: FOURIER SPACE / Details: local searches 0.9 degree with mask / Num. of class averages: 1 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 49.9714 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OH0 Pdb chain-ID: D / Accession code: 5OH0 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.85→2.85 Å / SU ML: 0.6831 / Cross valid method: FREE R-VALUE / σ(F): 9.88 / Phase error: 32.6199 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→81.14 Å
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Refine LS restraints |
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LS refinement shell |
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