Biological Assembly 1  

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.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 224.8 kDa 
• Atom Count: 9,582 
• Modelled Residue Count: 1,127 
• Deposited Residue Count: 1,920 
• Unique protein chains: 1

 7PFP

Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament

• PDB DOI: 10.2210/pdb7PFP/pdb
• EM Map EMD-13378: EMDB EMDataResource

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


• Deposited: 2021-08-11 Released: 2022-03-16 
• Deposition Author(s): Jovine, L., Xu, C., Stsiapanava, A., Carroni, M., Tunyasuvunakool, K., Jumper, J., Wu, B.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation, Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.

Stsiapanava, A., Xu, C., Nishio, S., Han, L., Yamakawa, N., Carroni, M., Tunyasuvunakool, K., Jumper, J., de Sanctis, D., Wu, B., Jovine, L.

(2022) Nat Struct Mol Biol 29: 190-193

• PubMed: 35273390 
• DOI: 10.1038/s41594-022-00729-3
• Primary Citation of Related Structures:  
  7P6R, 7P6S, 7P6T, 7PFP, 7Q3N


• PubMed Abstract: 
  

Glycoprotein 2 (GP2) and uromodulin (UMOD) filaments protect against gastrointestinal and urinary tract infections by acting as decoys for bacterial fimbrial lectin FimH. By combining AlphaFold2 predictions with X-ray crystallography and cryo-EM, we show that these proteins contain a bipartite decoy module whose new fold presents the high-mannose glycan recognized by FimH. The structure rationalizes UMOD mutations associated with kidney diseases and visualizes a key epitope implicated in cast nephropathy.

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Related Citations: 

• 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

• Identification and characterization of D8C, a novel domain present in liver-specific LZP, uromodulin and glycoprotein 2, mutated in familial juvenile hyperuricaemic nephropathy.
  Yang, H., Wu, C., Zhao, S., Guo, J.
  (2004) FEBS Lett 578: 236

• 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

• 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., Bokhove, M., Han, L., Hebert, H., Carroni, M., Yasumasu, S., Rampoldi, L., Wu, B., Jovine, L.
  (2020) EMBO J 39: e106807

• Highly accurate protein structure prediction with AlphaFold.
  Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Zidek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S.A.A., Ballard, A.J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A.W., Kavukcuoglu, K., Kohli, P., Hassabis, D.
  (2021) Nature --: --

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Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uromodulin	A, B, C	640	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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	F, N	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G36191CD GlyCosmos:  G36191CD GlyGen:  G36191CD

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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, O	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ GlyCosmos:  G80966KZ GlyGen:  G80966KZ

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H, P	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 7
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)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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	I, Q	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46638GC GlyCosmos:  G46638GC GlyGen:  G46638GC

Entity ID: 8
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.5
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Jovine, L., Xu, C., Stsiapanava, A., Carroni, M., Tunyasuvunakool, K., Jumper, J., Wu, B.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-03999
Swedish Research Council	Sweden	2020-04936
Knut and Alice Wallenberg Foundation	Sweden	2018.0042
Ministry of Education (MoE, Singapore)	Sweden	MOH-000382-00

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Database references
• Version 1.2: 2022-03-30
  Changes: Database references