Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 154.56 kDa 
• Atom Count: 10573 
• Residue Count: 1356 
• Unique protein chains: 1

4WRN

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

• DOI: 10.2210/pdb4WRN/pdb

• 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

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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 

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:  
  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 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: 

• 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

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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
Maltose-binding periplasmic protein,Uromodulin	A, B	695	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 17  Gene Names: malE, Z5632, ECs5017
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide /  Nutrient		--

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 = 242.32	α = 90
b = 242.32	β = 90
c = 258.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-10-24 
• Released Date: 2016-01-27 
Deposition Author(s): Bokhove, M., De Sanctis, D., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Center for Biosciences	Sweden	--
Swedish Research Council	Sweden	2012-5093
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
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary