+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7342 | |||||||||
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Title | Cryo-EM structure of the Type 1 pilus rod | |||||||||
Map data | Cryo-EM structure of Type 1 pilus rod | |||||||||
Sample |
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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 K-12 (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Zheng W / Wang F / Luna-Rico A / Francetic O / Hultgren SJ / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2018 Title: Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions. Authors: Caitlin N Spaulding / Henry Louis Schreiber / Weili Zheng / Karen W Dodson / Jennie E Hazen / Matt S Conover / Fengbin Wang / Pontus Svenmarker / Areli Luna-Rico / Olivera Francetic / Magnus ...Authors: Caitlin N Spaulding / Henry Louis Schreiber / Weili Zheng / Karen W Dodson / Jennie E Hazen / Matt S Conover / Fengbin Wang / Pontus Svenmarker / Areli Luna-Rico / Olivera Francetic / Magnus Andersson / Scott Hultgren / Edward H Egelman / Abstract: Uropathogenic (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating ...Uropathogenic (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating FimA subunits, provides a structural scaffold for displaying the tip adhesin, FimH. We solved the 4.2 Å resolution structure of the type 1 pilus rod using cryo-electron microscopy. Residues forming the interactive surfaces that determine the mechanical properties of the rod were maintained by selection based on a global alignment of sequences. We identified mutations that did not alter pilus production in vitro but reduced the force required to unwind the rod. UPEC expressing these mutant pili were significantly attenuated in bladder infection and intestinal colonization in mice. This study elucidates an unappreciated functional role for the molecular spring-like property of type 1 pilus rods in host-pathogen interactions and carries important implications for other pilus-mediated diseases. | |||||||||
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_7342.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-7342-v30.xml emd-7342.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_7342.png | 173.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7342 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7342 | HTTPS FTP |
-Validation report
Summary document | emd_7342_validation.pdf.gz | 482.8 KB | Display | EMDB validaton report |
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Full document | emd_7342_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | emd_7342_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_7342_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7342 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7342 | HTTPS FTP |
-Related structure data
Related structure data | 6c53MC 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_7342.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Type 1 pilus rod | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Type 1 pilus
Entire | Name: Type 1 pilus |
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Components |
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-Supramolecule #1: Type 1 pilus
Supramolecule | Name: Type 1 pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli K-12 (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: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Molecular weight | Theoretical: 15.835243 KDa |
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 | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 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: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 7.7 Å Applied symmetry - Helical parameters - Δ&Phi: 115 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 72627 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: OTHER / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: SPIDER |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6c53: |