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Open data
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Basic information
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Title | 2.7 A cryo-EM structure of in vitro assembled type 1 pilus rod | |||||||||||||||
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![]() | FimA / ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Function / homology | Fimbrial-type adhesion domain / Fimbrial protein / cell adhesion involved in single-species biofilm formation / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / ![]() ![]() ![]() | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | helical reconstruction / ![]() | |||||||||||||||
![]() | Hospenthal M / Zyla D / Glockshuber R / Waksman G | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
Images | ![]() | 54.3 KB | ||
Masks | ![]() | 59.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 46.2 MB 46.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8psvMC ![]() 6y7sC ![]() 8ptuC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: halfmap1
File | emd_17863_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
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Density Histograms |
-Half map: halfmap2
File | emd_17863_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
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Sample components
-Entire : Type 1 pilus rod
Entire | Name: Type 1 pilus rod |
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Components |
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-Supramolecule #1: Type 1 pilus rod
Supramolecule | Name: Type 1 pilus rod / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Type 1 pili assembled in vitro from recombinantly expressed as inclusion bodies and refolded FimA. |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 20.3 kDa/nm |
-Macromolecule #1: Type-1 fimbrial protein, A chain
Macromolecule | Name: Type-1 fimbrial protein, A chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 18.121074 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MKIKTLAIVV LSALSLSSTA ALAAATTVNG GTVHFKGEVV NAACAVDAGS VDQTVQLGQV RTASLAQEGA TSSAVGFNIQ LNDCDTNVA SKAAVAFLGT AIDAGHTNVL ALQSSAAGSA TNVGVQILDR TGAALTLDGA TFSSETTLNN GTNTIPFQAR Y FATGAATP GAANADATFK VQYQ UniProtKB: Type-1 fimbrial protein, A chain |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 1.58 mg/mL |
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Buffer | pH: 7 / Details: in ddH2O. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 3 ul sample, 30 s wait time, 0.5 s drain time, 6 s blotting. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 8000 pixel / Digitization - Dimensions - Height: 8000 pixel / Number grids imaged: 1 / Average exposure time: 14.0 sec. / Average electron dose: 97.54 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Segment selection | Number selected: 516000 Details: Autopicking based on the 2D classes from manually chosen filaments |
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Startup model | Type of model: OTHER / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 3.08) |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 7.76 Å Applied symmetry - Helical parameters - Δ&Phi: 115.0 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 11000 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: D / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 45.07 / Target criteria: Correlation coefficient |
Output model | ![]() PDB-8psv: |