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- EMDB-11141: Cryo-electron tomogram of urine from patient with K. pneumoniae u... -

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Basic information

Entry
Database: EMDB / ID: EMD-11141
TitleCryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection
Map dataCryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection
Sample
  • Complex: Cryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection
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_11141.png

Downloads & links

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Map

FileDownload / File: emd_11141.map.gz / Format: CCP4 / Size: 708.8 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection
Voxel sizeX=Y=Z: 18.28 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)14.55448 (±17.512655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin208-208252
Dimensions14401024504
Spacing10241440504
CellA: 18718.72 Å / B: 26323.201 Å / C: 9213.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z18.28000097656318.28000069444418.28
M x/y/z10241440504
origin x/y/z0.0000.0000.000
length x/y/z18718.72126323.2019213.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-208208252
NC/NR/NS10241440504
D min/max/mean-128.000127.00014.554

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Supplemental data

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Sample components

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Entire : Cryo-electron tomogram of urine from patient with K. pneumoniae u...

EntireName: Cryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection
Components
  • Complex: Cryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection

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Supramolecule #1: Cryo-electron tomogram of urine from patient with K. pneumoniae u...

SupramoleculeName: Cryo-electron tomogram of urine from patient with K. pneumoniae urinary tract infection
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
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 160.0 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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