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Yorodumi- EMDB-3809: The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Us... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3809 | |||||||||
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Title | The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli J96 (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Hospenthal MK / Costa TRD / Redzej A / Waksman G | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2017 Title: The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod. Authors: Manuela K Hospenthal / Dawid Zyla / Tiago R D Costa / Adam Redzej / Christoph Giese / James Lillington / Rudi Glockshuber / Gabriel Waksman / Abstract: Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play ...Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3809.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-3809-v30.xml emd-3809.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_3809.png | 273.9 KB | ||
Masks | emd_3809_msk_1.map | 52.7 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3809 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3809 | HTTPS FTP |
-Validation report
Summary document | emd_3809_validation.pdf.gz | 260.9 KB | Display | EMDB validaton report |
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Full document | emd_3809_full_validation.pdf.gz | 260.1 KB | Display | |
Data in XML | emd_3809_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3809 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3809 | HTTPS FTP |
-Related structure data
Related structure data | 5oh0MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3809.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_3809_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type 1 Chaperone-usher pilus
Entire | Name: Type 1 Chaperone-usher pilus |
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Components |
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-Supramolecule #1: Type 1 Chaperone-usher pilus
Supramolecule | Name: Type 1 Chaperone-usher pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Superhelical assembly of the pilus rod subunit FimA |
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Source (natural) | Organism: Escherichia coli J96 (bacteria) |
Recombinant expression | Organism: Escherichia coli HB101 (bacteria) |
-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 J96 (bacteria) |
Molecular weight | Theoretical: 15.835243 KDa |
Recombinant expression | Organism: Escherichia coli HB101 (bacteria) |
Sequence | String: AATTVNGGTV HFKGEVVNAA CAVDAGSVDQ TVQLGQVRTA SLAQEGATSS AVGFNIQLND CDTNVASKAA VAFLGTAIDA GHTNVLALQ SSAAGSATNV GVQILDRTGA ALTLDGATFS SETTLNNGTN TIPFQARYFA TGAATPGAAN ADATFKVQYQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 / Component:
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Grid | Model: Quantifoil 1.2/1.3 400 mesh grid / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |