9NU3 | pdb_00009nu3

Uromodulin filament lattice in the kinked arrangement from human urine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of human uromodulin filament networks in uropathogen capture.

Chang, A.N.Cerutti, G.Ogawa, Y.Basler, A.Switzer, W.Eng-Kohn, M.Lee, C.Fitzpatrick, A.W.P.

(2025) Structure 33: 1186-1192.e3

  • DOI: https://doi.org/10.1016/j.str.2025.04.011
  • Primary Citation of Related Structures:  
    9NU1, 9NU2, 9NU3

  • PubMed 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 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.


  • Organizational Affiliation
    • Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uromodulin640Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07911 (Homo sapiens)
Explore P07911 
Go to UniProtKB:  P07911
PHAROS:  P07911
GTEx:  ENSG00000169344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07911
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P07911-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
CA [auth c],
CB [auth 2],
DA [auth d],
AA [auth a],
AB [auth 0],
CA [auth c],
CB [auth 2],
DA [auth d],
DB [auth 3],
EB [auth 4],
FA [auth f],
FB [auth 5],
GA [auth g],
IA [auth i],
KA [auth k],
MA [auth m],
NA [auth n],
PA [auth p],
QA [auth q],
RA [auth r],
S,
TA [auth t],
U,
UA [auth u],
V,
X,
XA [auth x],
Z,
ZA [auth z]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
BA [auth b],
BB [auth 1],
EA [auth e],
HA [auth h],
JA [auth j],
BA [auth b],
BB [auth 1],
EA [auth e],
HA [auth h],
JA [auth j],
LA [auth l],
OA [auth o],
SA [auth s],
T,
VA [auth v],
W,
WA [auth w],
Y,
YA [auth y]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
GB [auth C]
HB [auth A]
IB [auth D]
JB [auth E]
KB [auth J]
GB [auth C],
HB [auth A],
IB [auth D],
JB [auth E],
KB [auth J],
LB [auth G],
MB [auth B],
NB [auth N],
OB [auth P],
PB [auth K],
QB [auth I],
RB [auth O],
SB [auth Q]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references