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- EMDB-11138: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates -

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Basic information

Entry
Database: EMDB / ID: EMD-11138
TitleCryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Map dataCryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Sample
  • Complex: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsWeiss 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
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255 Switzerland
Swiss National Science Foundation310030B_176403/1 Switzerland
European Research Council (ERC)679209 Switzerland
Swiss National Science Foundation31003A_169850 Switzerland
Swiss National Science Foundation31003A_156304 Switzerland
Swiss National Science FoundationPZ00P3_183777 Switzerland
Swiss National Science FoundationPZ00P3_161147 Switzerland
CitationJournal: 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
DepositionJun 6, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_11138.png

Downloads & links

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Map

FileDownload / File: emd_11138.map.gz / Format: CCP4 / Size: 280.4 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Voxel sizeX=Y=Z: 17.2 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)-2.0872042 (±22.260828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616165
Dimensions928960330
Spacing960928330
CellA: 16512.0 Å / B: 15961.601 Å / C: 5676.0005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z17.217.20000107758617.2
M x/y/z960928330
origin x/y/z0.0000.0000.000
length x/y/z16512.00015961.6015676.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS16-16165
NC/NR/NS960928330
D min/max/mean-128.000127.000-2.087

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Supplemental data

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Sample components

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Entire : Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates

EntireName: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
Components
  • Complex: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates

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Supramolecule #1: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates

SupramoleculeName: Cryo-electron tomogram of FIB milled E.coli - Uromodulin aggregates
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 8.2
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused 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 markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 140.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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