Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 188.75 kDa 
• Atom Count: 4918 
• Modelled Residue Count: 593 
• Deposited Residue Count: 1689 
• Unique protein chains: 1

6TQK

Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.

• PDB DOI: 10.2210/pdb6TQK/pdb
• EM Map EMD-10553:EMDBEMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2019-12-16 Released: 2020-11-04 
• Deposition Author(s): Stsiapanava, A., Xu, C., Carroni, M., Wu, B., Jovine, L.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation, Ministry of Education (MoE, Singapore)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM structure of native human uromodulin, a zona pellucida module polymer.

Stsiapanava, A., Xu, C., Brunati, M., Zamora-Caballero, S., Schaeffer, C., Bokhove, M., Han, L., Hebert, H., Carroni, M., Yasumasu, S., Rampoldi, L., Wu, B., Jovine, L.

(2020) EMBO J 39: e106807-e106807

• PubMed: 33196145 
• DOI: 10.15252/embj.2020106807
• Primary Citation of Related Structures:  
  6TQK, 6TQL


• PubMed Abstract: 
  

Assembly of extracellular filaments and matrices mediating fundamental biological processes such as morphogenesis, hearing, fertilization, and antibacterial defense is driven by a ubiquitous polymerization module known as zona pellucida (ZP) "domain". Despite the conservation of this element from hydra to humans, no detailed information is available on the filamentous conformation of any ZP module protein. Here, we report a cryo-electron microscopy study of uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant protein in human urine and an archetypal ZP module-containing molecule, in its mature homopolymeric state. UMOD forms a one-start helix with an unprecedented 180-degree twist between subunits enfolded by interdomain linkers that have completely reorganized as a result of propeptide dissociation. Lateral interaction between filaments in the urine generates sheets exposing a checkerboard of binding sites to capture uropathogenic bacteria, and UMOD-based models of heteromeric vertebrate egg coat filaments identify a common sperm-binding region at the interface between subunits.

---

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

• Etude chimique et ultrastructurale de la glycoproteine de Tamm et Horsfall ou uromucoide.
  Delain, E., Thiery, J.P., Coulard, D., Joliviene, A., Hartman, L.
  (1980) Biol Cellulaire 39: 31

• Identification of human uromodulin as the Tamm-Horsfall urinary glycoprotein.
  Pennica, D., Kohr, W.J., Kuang, W.J., Glaister, D., Aggarwal, B.B., Chen, E.Y., Goeddel, D.V.
  (1987) Science 236: 83

• 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

• Analysis of uromodulin polymerization provides new insights into the mechanisms regulating ZP domain-mediated protein assembly.
  Schaeffer, C., Santambrogio, S., Perucca, S., Casari, G., Rampoldi, L.
  (2009) Mol Biol Cell 20: 589

• 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

• The serine protease hepsin mediates urinary secretion and polymerisation of Zona Pellucida domain protein uromodulin.
  Brunati, M., Perucca, S., Han, L., Cattaneo, A., Consolato, F., Andolfo, A., Schaeffer, C., Olinger, E., Peng, J., Santambrogio, S., Perrier, R., Li, S., Bokhove, M., Bachi, A., Hummler, E., Devuyst, O., Wu, Q., Jovine, L., Rampoldi, L.
  (2015) Elife 4: e08887

• 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

• Structure of zona pellucida module proteins.
  Bokhove, M., Jovine, L.
  (2018) Curr Top Dev Biol 130: 413

• Cryo-EM structure of native human uromodulin, a zona pellucida module polymer.
  Stsiapanava, A., Xu, C., Brunati, M., Zamora-Caballero, S., Schaeffer, C., Han, L., Carroni, M., Yasumasu, S., Rampoldi, L., Wu, B., Jovine, L.
  (2020) Biorxiv --: --

---

Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uromodulin	A, B, C	563	Homo sapiens	Mutation(s): 0  Gene Names: UMOD
UniProt & NIH Common Fund Data Resources
Find proteins for P07911 (Homo sapiens) Explore P07911  Go to UniProtKB:  P07911
PHAROS:  P07911 GTEx:  ENSG00000169344

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G24420RT GlyCosmos:  G24420RT GlyGen:  G24420RT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-12-16 
• Released Date: 2020-11-04 
Deposition Author(s): Stsiapanava, A., Xu, C., Carroni, M., Wu, B., Jovine, L.

---

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-03999
Knut and Alice Wallenberg Foundation	Sweden	2018.0042
Ministry of Education (MoE, Singapore)	Singapore	2017-T1-001-168
Ministry of Education (MoE, Singapore)	Singapore	2016-T2-1-010

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2020-12-09
  Changes: Structure summary
• Version 1.3: 2020-12-16
  Changes: Database references
• Version 1.4: 2021-03-03
  Changes: Database references