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- EMDB-11133: Subtomogram average of human Uromodulin filaments incubated with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11133
TitleSubtomogram average of human Uromodulin filaments incubated with FimH lectin domain
Map dataSubtomogram average of human Uromodulin incubated with FimH lectin domain
Sample
  • Complex: human Uromodulin incubated with FimH lectin domain
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 16.6 Å
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
  • Surface view with section colored by density value
  • Surface level: 0.643
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.643
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11133.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of human Uromodulin incubated with FimH lectin domain
Voxel sizeX=Y=Z: 3.449 Å
Density
Contour LevelBy AUTHOR: 0.643 / Movie #1: 0.643
Minimum - Maximum-3.421444 - 7.4256935
Average (Standard dev.)-0.23042946 (±0.69707507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 275.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.4493.4493.449
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z275.920275.920275.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-3.4217.426-0.230

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Supplemental data

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Mask #1

Fileemd_11133_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map for FSC calculation (even)

Fileemd_11133_half_map_1.map
Annotationhalf map for FSC calculation (even)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: hald map for FSC calculation (odd)

Fileemd_11133_half_map_2.map
Annotationhald map for FSC calculation (odd)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : human Uromodulin incubated with FimH lectin domain

EntireName: human Uromodulin incubated with FimH lectin domain
Components
  • Complex: human Uromodulin incubated with FimH lectin domain

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Supramolecule #1: human Uromodulin incubated with FimH lectin domain

SupramoleculeName: human Uromodulin incubated with FimH lectin domain / 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
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 8.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 45 / Number images used: 10975
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 5340

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