+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11129 | ||||||||||||||||||||||||
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Title | Subtomogram average of human Uromodulin filaments | ||||||||||||||||||||||||
Map data | Subtomogram average of human Uromodulin filaments | ||||||||||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 15.6 Å | ||||||||||||||||||||||||
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
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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 |
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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_11129.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-11129-v30.xml emd-11129.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_11129.png | 37.9 KB | ||
Masks | emd_11129_msk_1.map | 501 KB | Mask map | |
Others | emd_11129_half_map_1.map.gz emd_11129_half_map_2.map.gz | 277 KB 250.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11129 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11129 | HTTPS FTP |
-Validation report
Summary document | emd_11129_validation.pdf.gz | 419.9 KB | Display | EMDB validaton report |
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Full document | emd_11129_full_validation.pdf.gz | 419.1 KB | Display | |
Data in XML | emd_11129_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11129 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11129 | HTTPS FTP |
-Related structure data
Related structure data | 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_11129.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of human Uromodulin filaments | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.449 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_11129_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map for FSC calculations (odd)
File | emd_11129_half_map_1.map | ||||||||||||
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Annotation | half map for FSC calculations (odd) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map for FSC calculations (even)
File | emd_11129_half_map_2.map | ||||||||||||
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Annotation | half map for FSC calculations (even) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human Uromodulin
Entire | Name: human Uromodulin |
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Components |
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-Supramolecule #1: human Uromodulin
Supramolecule | Name: human Uromodulin / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 81.5 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8.2 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 80.0 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 | Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 18299 |
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Extraction | Number tomograms: 19 / Number images used: 31027 |
Final angle assignment | Type: NOT APPLICABLE |