4WRN

Crystal structure of the polymerization region of human uromodulin/Tamm-Horsfall protein

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Escherichia coli O157:H7, Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2014-10-24 Released: 2016-01-27 
  • Deposition Author(s): Bokhove, M., De Sanctis, D., Jovine, L.
  • Funding Organization(s): Karolinska Institutet, Center for Biosciences, Swedish Research Council, Gustafsson Foundation for Research in Natural Sciences and Medicine, Sven and Ebba-Christina Hagberg foundation, European Molecular Biology Organization, European Union

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report



Literature

A structured interdomain linker directs self-polymerization of human uromodulin.

Bokhove, M.Nishimura, K.Brunati, M.Han, L.de Sanctis, D.Rampoldi, L.Jovine, L.

(2016) Proc Natl Acad Sci U S A 113: 1552-1557

  • DOI: 10.1073/pnas.1519803113
  • Primary Citation of Related Structures:  
    5BUP, 4WRN

  • PubMed Abstract: 
  • Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extr ...

    Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extracellular filaments that regulate kidney electrolyte balance and innate immunity, as well as protect against renal stones. Moreover, salt-dependent aggregation of UMOD filaments in the urine generates a soluble molecular net that captures uropathogenic bacteria and facilitates their clearance. Despite the functional importance of its homopolymers, no structural information is available on UMOD and how it self-assembles into filaments. Here, we report the crystal structures of polymerization regions of human UMOD and mouse ZP2, an essential sperm receptor protein that is structurally related to UMOD but forms heteropolymers. The structure of UMOD reveals that an extensive hydrophobic interface mediates ZP-N domain homodimerization. This arrangement is required for filament formation and is directed by an ordered ZP-N/ZP-C linker that is not observed in ZP2 but is conserved in the sequence of deafness/Crohn's disease-associated homopolymeric glycoproteins α-tectorin (TECTA) and glycoprotein 2 (GP2). Our data provide an example of how interdomain linker plasticity can modulate the function of structurally similar multidomain proteins. Moreover, the architecture of UMOD rationalizes numerous pathogenic mutations in both UMOD and TECTA genes.


    Related Citations: 
    • Characterization and separation of an inhibitor of viral hemagglutination present in urine.
      Tamm, I., Horsfall, F.L.
      (1950) Proc Soc Exp Biol Med 74: 106
    • Isolation of the cDNA encoding glycoprotein-2 (GP-2), the major zymogen granule membrane protein. Homology to uromodulin/Tamm-Horsfall protein.
      Hoops, T.C., Rindler, M.J.
      (1991) J Biol Chem 266: 4257
    • Mutations in the human alpha-tectorin gene cause autosomal dominant non-syndromic hearing impairment.
      Verhoeven, K., Van Laer, L., Kirschhofer, K., Legan, P.K., Hughes, D.C., Schatteman, I., Verstreken, M., Van Hauwe, P., Coucke, P., Chen, A., Smith, R.J., Somers, T., Offeciers, F.E., Van de Heyning, P., Richardson, G.P., Wachtler, F., Kimberling, W.J., Willems, P.J., Govaerts, P.J., Van Camp, G.
      (1998) Nat Genet 19: 60
    • The ZP domain is a conserved module for polymerization of extracellular proteins.
      Jovine, L., Qi, H., Williams, Z., Litscher, E., Wassarman, P.M.
      (2002) Nat Cell Biol 4: 457
    • Tamm-Horsfall glycoprotein: biology and clinical relevance.
      Serafini-Cessi, F., Malagolini, N., Cavallone, D.
      (2003) Am J Kidney Dis 42: 658
    • A duplicated motif controls assembly of zona pellucida domain proteins.
      Jovine, L., Qi, H., Williams, Z., Litscher, E.S., Wassarman, P.M.
      (2004) Proc Natl Acad Sci U S A 101: 5922
    • Zona pellucida domain proteins.
      Jovine, L., Darie, C.C., Litscher, E.S., Wassarman, P.M.
      (2005) Annu Rev Biochem 74: 83
    • Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
      Han, L., Monne, M., Okumura, H., Schwend, T., Cherry, A.L., Flot, D., Matsuda, T., Jovine, L.
      (2010) Cell 143: 404
    • The rediscovery of uromodulin (Tamm-Horsfall protein): from tubulointerstitial nephropathy to chronic kidney disease.
      Rampoldi, L., Scolari, F., Amoroso, A., Ghiggeri, G., Devuyst, O.
      (2011) Kidney Int 80: 338

    Organizational Affiliation

    Department of Biosciences and Nutrition & Center for Innovative Medicine, Karolinska Institutet, SE-141 83 Huddinge, Sweden; luca.jovine@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,UromodulinAB695Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 17 
Gene Names: malEZ5632ECs5017
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C, D
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
C, Dalpha-maltoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.32α = 90
b = 242.32β = 90
c = 258.86γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Karolinska InstitutetSweden--
Center for BiosciencesSweden--
Swedish Research CouncilSweden2012-5093
Gustafsson Foundation for Research in Natural Sciences and MedicineSweden--
Sven and Ebba-Christina Hagberg foundationSweden--
European Molecular Biology Organization--
European UnionERC 260759

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2016-02-17
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary