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- EMDB-11388: 3.5 A cryo-EM structure of human uromodulin filament core -

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Basic information

Entry
Database: EMDB / ID: EMD-11388
Title3.5 A cryo-EM structure of human uromodulin filament core
Map data
SampleNative human uromodulin filament core:
Uromodulin
Function / homology
Function and homology information


neutrophil migration / ciliary membrane / IgG binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / extracellular matrix structural constituent / extrinsic component of membrane / cellular defense response / anchored component of membrane / cilium ...neutrophil migration / ciliary membrane / IgG binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / extracellular matrix structural constituent / extrinsic component of membrane / cellular defense response / anchored component of membrane / cilium / spindle pole / Golgi lumen / basolateral plasma membrane / apical plasma membrane / negative regulation of cell population proliferation / calcium ion binding / cell surface / extracellular space / extracellular exosome
EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding domain / EGF-like domain / Zona pellucida domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like calcium-binding, conserved site / Zona pellucida domain, conserved site / EGF domain
Uromodulin
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsStanisich JJ / Zyla D / Afanasyev P / Xu J / Pilhofer M / Boeringer D / Glockshuber R
Funding support Switzerland, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_176403/1 Switzerland
Swiss National Science Foundation31003A_179255 Switzerland
Swiss National Science Foundation31003A_156304 Switzerland
European Research Council (ERC)679209 Switzerland
CitationJournal: Elife / Year: 2020
Title: The cryo-EM structure of the human uromodulin filament core reveals a unique assembly mechanism.
Authors: Jessica J Stanisich / Dawid S Zyla / Pavel Afanasyev / Jingwei Xu / Anne Kipp / Eric Olinger / Olivier Devuyst / Martin Pilhofer / Daniel Boehringer / Rudi Glockshuber /
Abstract: The glycoprotein uromodulin (UMOD) is the most abundant protein in human urine and forms filamentous homopolymers that encapsulate and aggregate uropathogens, promoting pathogen clearance by urine ...The glycoprotein uromodulin (UMOD) is the most abundant protein in human urine and forms filamentous homopolymers that encapsulate and aggregate uropathogens, promoting pathogen clearance by urine excretion. Despite its critical role in the innate immune response against urinary tract infections, the structural basis and mechanism of UMOD polymerization remained unknown. Here, we present the cryo-EM structure of the UMOD filament core at 3.5 Å resolution, comprised of the bipartite zona pellucida (ZP) module in a helical arrangement with a rise of ~65 Å and a twist of ~180°. The immunoglobulin-like ZPN and ZPC subdomains of each monomer are separated by a long linker that interacts with the preceding ZPC and following ZPN subdomains by β-sheet complementation. The unique filament architecture suggests an assembly mechanism in which subunit incorporation could be synchronized with proteolytic cleavage of the C-terminal pro-peptide that anchors assembly-incompetent UMOD precursors to the membrane.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 15, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 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: 1
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  • Surface view colored by cylindrical radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-6zs5
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-6zya
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zs5
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zya
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11388.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 346.88 Å
1.08 Å/pix.
x 320 pix.
= 346.88 Å
1.08 Å/pix.
x 320 pix.
= 346.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 1 / Movie #1: 1
Minimum - Maximum-2.3153067 - 6.7981424
Average (Standard dev.)0.000833728 (±0.081922434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z346.880346.880346.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.3156.7980.001

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Supplemental data

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Segmentation: #1

Fileemd_11388_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: density modified main map

Fileemd_11388_additional.map
Annotationdensity modified main map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: half map B

Fileemd_11388_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map B

Fileemd_11388_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Sample components

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Entire Native human uromodulin filament core

EntireName: Native human uromodulin filament core
Details: Native uromodulin was purified from healthy human urine.
Number of components: 2

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Component #1: protein, Native human uromodulin filament core

ProteinName: Native human uromodulin filament core
Details: Native uromodulin was purified from healthy human urine.
Recombinant expression: No
MassExperimental: 1.28 MDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Uromodulin

ProteinName: Uromodulin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 69.82168 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Sample solutionSpecimen conc.: 1.58 mg/mL / pH: 8.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 282 K / Humidity: 95 %
Details: 3.5 ul sample, 30 s wait time, 0.5 s drain time, 13.5 s blotting from the back.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 3300.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 9543 / Details: Data was joined from two sessions

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 145000 / Details: Motion correction with dose-weighting
3D reconstructionSoftware: cryoSPARC / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 4WRN
Chain ID: A

Overall bvalue: 49.9714
Output model

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