7Q3N | pdb_00007q3n

Cryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the FimH lectin domain from uropathogenic E. coli

• PDB DOI: https://doi.org/10.2210/pdb7Q3N/pdb
• EM Map EMD-13794: EMDB EMDataResource

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens, Escherichia coli UTI89
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-10-28 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: 7.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

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: https://doi.org/10.1038/s41594-022-00729-3
• Primary Citation 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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Organizational Affiliation: 
• Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
US 41-UMS 2014-PLBS, Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France.
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
DeepMind, London, UK.
ESRF - The European Synchrotron, Grenoble, France.
Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. [e-mail].
School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.88 kDa 
• Atom Count: 3,599 
• Modeled Residue Count: 451 
• Deposited Residue Count: 735 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uromodulin	A [auth U]	563	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07911 (Homo sapiens) Explore P07911  Go to UniProtKB:  P07911
PHAROS:  P07911 GTEx:  ENSG00000169344
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P07911-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 1 fimbiral adhesin FimH	B [auth F]	172	Escherichia coli UTI89	Mutation(s): 1  Gene Names: fimH, UTI89_C5017
UniProt
Find proteins for Q1R2J4 (Escherichia coli (strain UTI89 / UPEC)) Explore Q1R2J4  Go to UniProtKB:  Q1R2J4

Oligosaccharides

Help  

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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	E [auth C]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G66937TJ GlyCosmos: G66937TJ GlyGen: G66937TJ

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	F [auth D]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
MAN	BindingDB:  7Q3N	Kd: 2300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.08
MODEL REFINEMENT	PHENIX	1.19.2-4158

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	Singapore	2016-03999
Swedish Research Council	Singapore	2020-04936
Knut and Alice Wallenberg Foundation	Singapore	2018.0042
Ministry of Education (MoE, Singapore)	Singapore	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
• Version 1.3: 2024-10-23
  Changes: Data collection, Refinement description, Structure summary