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- PDB-9nu2: Uromodulin filament lattice in the straight arrangement from huma... -

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Basic information

Entry
Database: PDB / ID: 9nu2
TitleUromodulin filament lattice in the straight arrangement from human urine
ComponentsUromodulin
KeywordsANTIMICROBIAL PROTEIN / Kidney / urine / uropathogen / filament / lattice / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsChang, A.N. / Fitzpatrick, A.W.P.
Funding support1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Uromodulin
A: Uromodulin
B: Uromodulin
D: Uromodulin
E: Uromodulin
F: Uromodulin
K: Uromodulin
G: Uromodulin
I: Uromodulin
M: Uromodulin
O: Uromodulin
Q: Uromodulin
L: Uromodulin
H: Uromodulin
J: Uromodulin
N: Uromodulin
P: Uromodulin
R: Uromodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,282,79775
Polymers1,256,79018
Non-polymers26,00757
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Uromodulin / Tamm-Horsfall urinary glycoprotein / THP


Mass: 69821.680 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P07911
#2: Polysaccharide...
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Uromodulin filament lattice in the straight arrangement from human urine
Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 178.8 ° / Axial rise/subunit: 63.78 Å / Axial symmetry: C1
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 693160 / Symmetry type: HELICAL
RefinementHighest resolution: 4.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00347412
ELECTRON MICROSCOPYf_angle_d0.67564347
ELECTRON MICROSCOPYf_dihedral_angle_d6.4988679
ELECTRON MICROSCOPYf_chiral_restr0.0447371
ELECTRON MICROSCOPYf_plane_restr0.0048175

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