Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.00 kDa 
• Atom Count: 1349 
• Modelled Residue Count: 159 
• Deposited Residue Count: 213 
• Unique protein chains: 1

5BUP

Crystal structure of the ZP-C domain of mouse ZP2

• PDB DOI: 10.2210/pdb5BUP/pdb

• 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

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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 

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

• PubMed: 26811476 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida sperm-binding protein 2	A	213	Mus musculus	Mutation(s): 2  Gene Names: Zp2, Zp-2, Zpa
UniProt
Find proteins for P20239 (Mus musculus) Explore P20239  Go to UniProtKB:  P20239

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A], C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 = 105.21	α = 90
b = 105.21	β = 90
c = 40.55	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
Coot	model building
PHENIX	refinement
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-04 
• Released Date: 2016-01-27 
Deposition Author(s): Nishimura, K., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Center for Biosciences	Sweden	--
Swedish Research Council	Sweden	2012-5093
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine	Sweden	--
Sven and Ebba-Christina Hagberg foundation	Sweden	--
European Molecular Biology Organization		--
European Union		ERC 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