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- EMDB-11131: Subtomogram average of elastase treated human Uromodulin filament... -

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Basic information

Entry
Database: EMDB / ID: EMD-11131
TitleSubtomogram average of elastase treated human Uromodulin filaments (eUmod)
Map dataSubtomogram average of elastase treated human Uromodulin (eUmod)
Sample
  • Complex: elastase treated human Uromodulin filaments
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 17.3 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
European Research Council (ERC)679209 Switzerland
Swiss National Science Foundation310030B_176403/1 Switzerland
Swiss National Science Foundation31003A_156304 Switzerland
Swiss National Science Foundation31003A_169850 Switzerland
Swiss National Science FoundationPZ00P3_161147 Switzerland
Swiss National Science FoundationPZ00P3_183777 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-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11131.png

Downloads & links

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Map

FileDownload / File: emd_11131.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of elastase treated human Uromodulin (eUmod)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.45 Å/pix.
x 80 pix.
= 275.92 Å		3.45 Å/pix.
x 80 pix.
= 275.92 Å		3.45 Å/pix.
x 80 pix.
= 275.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.449 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.08 / Movie #1: 1.08
Minimum - Maximum-2.7261584 - 7.074093
Average (Standard dev.)-0.20075823 (±0.4952438)
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-2.7267.074-0.201

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Supplemental data

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Mask #1

Fileemd_11131_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map for FSC calculation (even)

Fileemd_11131_half_map_1.map
Annotationhalf map for FSC calculation (even)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map for FSC calculation (odd)

Fileemd_11131_half_map_2.map
Annotationhalf map for FSC calculation (odd)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : elastase treated human Uromodulin filaments

EntireName: elastase treated human Uromodulin filaments
Components
  • Complex: elastase treated human Uromodulin filaments

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Supramolecule #1: elastase treated human Uromodulin filaments

SupramoleculeName: elastase treated human Uromodulin filaments / 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
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 80.0 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2177
ExtractionNumber tomograms: 7 / Number images used: 6646
Final angle assignmentType: NOT APPLICABLE

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