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): 17 

  • 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: 3.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.USA 113: 1552-1557

  • DOI: 10.1073/pnas.1519803113
  • Primary Citation of Related Structures:  
  • Also Cited By: 5HZV

  • 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: 
    • Tamm-Horsfall glycoprotein: biology and clinical relevance.
      Serafini-Cessi, F.,Malagolini, N.,Cavallone, D.
      (2003) Am. J. Kidney Dis. 42: 658
    • 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
    • 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
    • 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
    • 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.USA 101: 5922
    • 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
    • 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
    • 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
    • Zona pellucida domain proteins.
      Jovine, L.,Darie, C.C.,Litscher, E.S.,Wassarman, P.M.
      (2005) Annu.Rev.Biochem. 74: 83


    Organizational Affiliation

    Department of Biosciences and Nutrition & Center for Innovative Medicine, Karolinska Institutet, SE-141 83 Huddinge, Sweden;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,Uromodulin
A, B
695Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 17 
Gene Names: malE, UMOD
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEY0
Find proteins for P07911 (Homo sapiens)
Go to Gene View: UMOD
Go to UniProtKB:  P07911
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A, B
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.221 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 242.320α = 90.00
b = 242.320β = 90.00
c = 258.860γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2016-02-17
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence