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Yorodumi- EMDB-17878: 2.5 A cryo-EM structure of the in vitro FimD-catalyzed assembly o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17878 | |||||||||||||||
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Title | 2.5 A cryo-EM structure of the in vitro FimD-catalyzed assembly of type 1 pilus rod | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | FimA / pilus / monomer / subunit / pili / main structural subunit / high resolution / STRUCTURAL PROTEIN / 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 | helical reconstruction / cryo EM / Resolution: 2.52 Å | |||||||||||||||
Authors | Zyla D / Hospenthal M / Glockshuber R / Waksman G | |||||||||||||||
Funding support | Switzerland, United Kingdom, 4 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17878.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-17878-v30.xml emd-17878.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_17878.png | 52.8 KB | ||
Masks | emd_17878_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-17878.cif.gz | 6.2 KB | ||
Others | emd_17878_half_map_1.map.gz emd_17878_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17878 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17878 | HTTPS FTP |
-Validation report
Summary document | emd_17878_validation.pdf.gz | 804.5 KB | Display | EMDB validaton report |
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Full document | emd_17878_full_validation.pdf.gz | 804.1 KB | Display | |
Data in XML | emd_17878_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_17878_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17878 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17878 | HTTPS FTP |
-Related structure data
Related structure data | 8ptuMC 6y7sC 8psvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17878.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_17878_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17878_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17878_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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 pilus rod assembled from FimA-FimC complexes in vitro in the presence of the usher FimD activated by FimG/FimF (250 molar excess of FimA-FimC over FimD) |
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Source (natural) | Organism: Escherichia coli (E. coli) |
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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 18.121074 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Number real images: 725 / Average exposure time: 7.0 sec. / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 47393 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number classes used: 1 Applied symmetry - Helical parameters - Δz: 7.8 Å Applied symmetry - Helical parameters - Δ&Phi: 115.0 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Details: standard Relion protocol / Number images used: 135000 |
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Segment selection | Number selected: 416000 / Software - Name: RELION Details: Autopicking based on the 2D classes from manually chosen filaments |
Startup model | Type of model: OTHER / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 3.08) |
-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: 46.49 / Target criteria: Correlation coefficient |
Output model | PDB-8ptu: |