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- EMDB-49794: Uromodulin filament lattice in the kinked arrangement from human urine -

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Basic information

Entry
Database: EMDB / ID: EMD-49794
TitleUromodulin filament lattice in the kinked arrangement from human urine
Map dataUromodulin filament lattice in the kinked arrangement from human urine
Sample
  • Tissue: Uromodulin filament lattice in the kinked arrangement from human urine
    • Protein or peptide: Uromodulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsKidney / urine / uropathogen / filament / lattice / ANTIMICROBIAL PROTEIN / kidney disease / UTI / urinary tract infection / infection
Function / homology
Function and homology information


citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / collecting duct development / urea transmembrane transport / metanephric ascending thin limb development ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / collecting duct development / urea transmembrane transport / metanephric ascending thin limb development / regulation of protein transport / micturition / protein localization to vacuole / intracellular chloride ion homeostasis / juxtaglomerular apparatus development / antibacterial innate immune response / renal urate salt excretion / urate transport / renal sodium ion absorption / glomerular filtration / neutrophil migration / intracellular phosphate ion homeostasis / response to water deprivation / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / IgG binding / extrinsic component of membrane / ciliary membrane / leukocyte cell-cell adhesion / cellular response to unfolded protein / multicellular organismal response to stress / cellular defense response / renal water homeostasis / side of membrane / tumor necrosis factor-mediated signaling pathway / ERAD pathway / : / RNA splicing / apoptotic signaling pathway / regulation of blood pressure / lipid metabolic process / autophagy / Golgi lumen / intracellular calcium ion homeostasis / spindle pole / defense response to Gram-negative bacterium / basolateral plasma membrane / response to lipopolysaccharide / cilium / apical plasma membrane / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / calcium ion binding / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane
Similarity search - Function
Uromodulin-like, D8C domain / EGF domain / EGF domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain ...Uromodulin-like, D8C domain / EGF domain / EGF domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / : / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsChang AN / Fitzpatrick AWP
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural basis of human uromodulin filament networks in uropathogen capture.
Authors: Andrew N Chang / Gabriele Cerutti / Yuki Ogawa / Alia Basler / Willa Switzer / Mia Eng-Kohn / Carolyn Lee / Anthony W P Fitzpatrick /
Abstract: Uromodulin (UMOD), the most abundant protein in human urine, is essential for kidney function and urinary tract health. UMOD forms filaments that bind to uropathogenic bacteria, facilitating their ...Uromodulin (UMOD), the most abundant protein in human urine, is essential for kidney function and urinary tract health. UMOD forms filaments that bind to uropathogenic bacteria, facilitating their aggregation and clearance from the urinary tract. Here, we present the cryo-electron microscopy (cryo-EM) structure of the bacteria-binding D10C domain of UMOD and reveal its binding to the filament core. The details of D10C-core binding explain the formation of distinct filament lattice architectures adopted by UMOD. The D10C-core binding interface gives rise to diverse filament lattice structures, ranging from open and expansive to compact and dense conformations, or a combination of both. We hypothesize that other molecules present in urine may act as cross-linking agents, further stabilizing this binding interface and facilitating the connection of individual filaments into larger networks capable of effectively trapping bacteria. Structural mapping of kidney disease-related mutations points toward the abolition of disulfide bonds and promotion of mutant UMOD aggregation.
History
DepositionMar 19, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49794.png

Downloads & links

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Map

FileDownload / File: emd_49794.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUromodulin filament lattice in the kinked arrangement from human urine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 386.64 Å		1.07 Å/pix.
x 360 pix.
= 386.64 Å		1.07 Å/pix.
x 360 pix.
= 386.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.174
Minimum - Maximum-0.34241116 - 0.93860483
Average (Standard dev.)0.0052839727 (±0.03980818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49794_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_49794_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Uromodulin filament lattice in the kinked arrangement from human urine

EntireName: Uromodulin filament lattice in the kinked arrangement from human urine
Components
  • Tissue: Uromodulin filament lattice in the kinked arrangement from human urine
    • Protein or peptide: Uromodulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Uromodulin filament lattice in the kinked arrangement from human urine

SupramoleculeName: Uromodulin filament lattice in the kinked arrangement from human urine
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Uromodulin

MacromoleculeName: Uromodulin / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.82168 KDa
SequenceString: MGQPSLTWML MVVVASWFIT TAATDTSEAR WCSECHSNAT CTEDEAVTTC TCQEGFTGDG LTCVDLDECA IPGAHNCSAN SSCVNTPGS FSCVCPEGFR LSPGLGCTDV DECAEPGLSH CHALATCVNV VGSYLCVCPA GYRGDGWHCE CSPGSCGPGL D CVPEGDAL ...String:
MGQPSLTWML MVVVASWFIT TAATDTSEAR WCSECHSNAT CTEDEAVTTC TCQEGFTGDG LTCVDLDECA IPGAHNCSAN SSCVNTPGS FSCVCPEGFR LSPGLGCTDV DECAEPGLSH CHALATCVNV VGSYLCVCPA GYRGDGWHCE CSPGSCGPGL D CVPEGDAL VCADPCQAHR TLDEYWRSTE YGEGYACDTD LRGWYRFVGQ GGARMAETCV PVLRCNTAAP MWLNGTHPSS DE GIVSRKA CAHWSGHCCL WDASVQVKAC AGGYYVYNLT APPECHLAYC TDPSSVEGTC EECSIDEDCK SNNGRWHCQC KQD FNITDI SLLEHRLECG ANDMKVSLGK CQLKSLGFDK VFMYLSDSRC SGFNDRDNRD WVSVVTPARD GPCGTVLTRN ETHA TYSNT LYLADEIIIR DLNIKINFAC SYPLDMKVSL KTALQPMVSA LNIRVGGTGM FTVRMALFQT PSYTQPYQGS SVTLS TEAF LYVGTMLDGG DLSRFALLMT NCYATPSSNA TDPLKYFIIQ DRCPHTRDST IQVVENGESS QGRFSVQMFR FAGNYD LVY LHCEVYLCDT MNEKCKPTCS GTRFRSGSVI DQSRVLNLGP ITRKGVQATV SRAFSSLGLL KVWLPLLLSA TLTLTFQ

UniProtKB: Uromodulin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 13 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1110345
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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