7P6S | pdb_00007p6s

Crystal structure of the FimH-binding decoy module of human glycoprotein 2 (GP2) (crystal form II)

• PDB DOI: https://doi.org/10.2210/pdb7P6S/pdb

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


• Deposited: 2021-07-17 Released: 2022-03-16 
• Deposition Author(s): Stsiapanava, A., Tunyasuvunakool, K., Jumper, J., de Sanctis, D., Jovine, L.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: 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: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.46 kDa 
• Atom Count: 1,389 
• Modeled Residue Count: 142 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Alpha of Pancreatic secretory granule membrane major glycoprotein GP2	A	161	Homo sapiens	Mutation(s): 0  Gene Names: GP2
UniProt & NIH Common Fund Data Resources
Find proteins for P55259 (Homo sapiens) Explore P55259  Go to UniProtKB:  P55259
PHAROS:  P55259 GTEx:  ENSG00000169347
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P55259-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
9JE	D [auth A]	pentane-1,5-diol C5 H12 O2 ALQSHHUCVQOPAS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.48	α = 90
b = 59.5	β = 90
c = 87.04	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
ISOLDE	refinement
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Stsiapanava, A., Tunyasuvunakool, K., Jumper, J., de Sanctis, D., Jovine, L.

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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

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: 2024-05-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary