5BUP

Crystal structure of the ZP-C domain of mouse ZP2

  • Classification: CELL ADHESION
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2015-06-04 Released: 2016-01-27 
  • Deposition Author(s): Nishimura, K., Jovine, L.
  • Funding Organization(s): Karolinska Institutet, Center for Biosciences, Swedish Research Council, Goran 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: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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 U S A 113: 1552-1557

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

  • 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: 
    • Synthesis of zona pellucida proteins by denuded and follicle-enclosed mouse oocytes during culture in vitro.
      Bleil, J.D., Wassarman, P.M.
      (1980) Proc Natl Acad Sci U S A 77: 1029
    • Mammalian sperm-egg interaction: fertilization of mouse eggs triggers modification of the major zona pellucida glycoprotein, ZP2.
      Bleil, J.D., Beall, C.F., Wassarman, P.M.
      (1981) Dev Biol 86: 189
    • Structural characterization of native mouse zona pellucida proteins using mass spectrometry.
      Boja, E.S., Hoodbhoy, T., Fales, H.M., Dean, J.
      (2003) J Biol Chem 278: 34189
    • Disulfide linkage patterns of pig zona pellucida glycoproteins ZP3 and ZP4.
      Kanai, S., Kitayama, T., Yonezawa, N., Sawano, Y., Tanokura, M., Nakano, M.
      (2008) Mol Reprod Dev 75: 847
    • 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

    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
Zona pellucida sperm-binding protein 2A213Mus musculusMutation(s): 2 
Gene Names: Zp2Zp-2Zpa
Find proteins for P20239 (Mus musculus)
Explore P20239 
Go to UniProtKB:  P20239
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.21α = 90
b = 105.21β = 90
c = 40.55γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Karolinska InstitutetSweden--
Center for BiosciencesSweden--
Swedish Research CouncilSweden2012-5093
Goran 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