[English] 日本語
Yorodumi- EMDB-11138: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11138 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates | ||||||||||||||||||||||||
Map data | Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates | ||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | electron tomography / cryo EM | ||||||||||||||||||||||||
Authors | Weiss GL / Stanisich JJ / Sauer MM / Lin C-W / Eras J / Zyla DS / Trueck J / Devuyst O / Aebi M / Pilhofer M / Glockshuber R | ||||||||||||||||||||||||
Funding support | Switzerland, 7 items
| ||||||||||||||||||||||||
Citation | Journal: Science / Year: 2020 Title: Architecture and function of human uromodulin filaments in urinary tract infections. Authors: Gregor L Weiss / Jessica J Stanisich / Maximilian M Sauer / Chia-Wei Lin / Jonathan Eras / Dawid S Zyla / Johannes Trück / Olivier Devuyst / Markus Aebi / Martin Pilhofer / Rudi Glockshuber / Abstract: Uromodulin is the most abundant protein in human urine, and it forms filaments that antagonize the adhesion of uropathogens; however, the filament structure and mechanism of protection remain poorly ...Uromodulin is the most abundant protein in human urine, and it forms filaments that antagonize the adhesion of uropathogens; however, the filament structure and mechanism of protection remain poorly understood. We used cryo-electron tomography to show that the uromodulin filament consists of a zigzag-shaped backbone with laterally protruding arms. N-glycosylation mapping and biophysical assays revealed that uromodulin acts as a multivalent ligand for the bacterial type 1 pilus adhesin, presenting specific epitopes on the regularly spaced arms. Imaging of uromodulin-uropathogen interactions in vitro and in patient urine showed that uromodulin filaments associate with uropathogens and mediate bacterial aggregation, which likely prevents adhesion and allows clearance by micturition. These results provide a framework for understanding uromodulin in urinary tract infections and in its more enigmatic roles in physiology and disease. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11138.map.gz | 227.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11138-v30.xml emd-11138.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_11138.png | 138.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11138 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11138 | HTTPS FTP |
-Validation report
Summary document | emd_11138_validation.pdf.gz | 211.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11138_full_validation.pdf.gz | 210.6 KB | Display | |
Data in XML | emd_11138_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11138 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11138 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_11138.map.gz / Format: CCP4 / Size: 280.4 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 17.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Entire | Name: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates |
---|---|
Components |
|
-Supramolecule #1: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Supramolecule | Name: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8.2 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 17 nA / Focused ion beam - Duration: 1800 sec. / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 3000 nm / Focused ion beam - Final thickness: 250 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Helios. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file. |
Fiducial marker | Manufacturer: Cytodiagnostics / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 140.0 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 | Number images used: 61 |
---|