7P6R

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

PDB DOI: https://doi.org/10.2210/pdb7P6R/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.281
R-Value Work: 0.234
R-Value Observed: 0.237

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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.

Organizational Affiliation

Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.

Macromolecule Content

Total Structure Weight: 37.49 kDa
Atom Count: 2,400
Modelled Residue Count: 265
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Alpha of Pancreatic secretory granule membrane major glycoprotein GP2	A, B	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
GTEx: ENSG00000169347
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55259
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P55259-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	C [auth A], D [auth A], E [auth A], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]