6TQL

Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 : e106807-e106807

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

  • 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" ...

    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.
      (2002) Nat Cell Biol 4: 457
    • Tamm-Horsfall glycoprotein: biology and clinical relevance.
      Wassarman, P.M., 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UromodulinABC296Homo sapiensMutation(s): 0 
Gene Names: UMOD
Find proteins for P07911 (Homo sapiens)
Explore P07911 
Go to UniProtKB:  P07911
NIH Common Fund Data Resources
PHAROS  P07911
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
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-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
10 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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
G
8 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03999
Knut and Alice Wallenberg FoundationSweden2018.0042
Ministry of Education (MoE, Singapore)Singapore2017-T1-001-168
Ministry of Education (MoE, Singapore)Singapore2016-T2-1-010

Revision History 

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references