8XC5 | pdb_00008xc5

Cryo-EM structure of GP2 fibrils derived from human pancreas

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

  • Deposited: 2023-12-08 Released: 2025-06-11 
  • Deposition Author(s): Cao, Q., Han, J.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human glycoprotein 2 reveals mechanisms underlying filament formation and adaption to proteolytic environment in the digestive tract.

Han, J.Song, M.Cheng, Y.Gong, W.Zhang, F.Cao, Q.

(2025) PLoS Biol 23: e3003238-e3003238

  • DOI: https://doi.org/10.1371/journal.pbio.3003238
  • Primary Citation of Related Structures:  
    8XC5

  • PubMed Abstract: 

    Glycoprotein 2 (GP2) and Uromodulin (UMOD) are considered as paralogs that share high sequence similarity and have similar antibacterial functions. UMOD are abundant as filaments in the urinary tract, and a high-mannose N-glycosylation site located on the N-terminal region protruding from UMOD filament core (referred to as branch) acts as an adhesion antagonist against pathogenic bacterial infections. The antibacterial function of UMOD can be eliminated by proteases, as the UMOD branch is susceptible to proteolytic activity. GP2 is expressed in the pancreas and secreted into the digestive tract. Whether GP2 executes its function in filament form and how it remains functional in the protease-enriched digestive tract is unclear. In this study, we extract GP2 filaments from surgically excised human pancreas and determined their cryo-EM structure. Our structure analysis unveiled that GP2 forms filaments with its ZP modules, composing the ZPN and ZPC domains along with a linker that connects these two domains. The N-terminal region (branch) of GP2 does not constitute the filament core and appears flexible in the cryo-EM structure. Our biochemical experiments suggested that although the GP2 branch is also protease-susceptible, additional high-mannose N-glycans were identified on the protease-resistant GP2 filament core. Consequently, the branch-free GP2 filaments retain their binding ability to the bacterial adhesin FimH, ensuring GP2's antibacterial function unaffected in the proteolytic environment. Our study provides the first experimental evidence of GP2 filament formation and reveals the molecular mechanisms underlying GP2's adaptation to a different environment compared to UMOD.


  • Organizational Affiliation
    • Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pancreatic secretory granule membrane major glycoprotein GP2
A, B, C
537Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P55259 (Homo sapiens)
Explore P55259 
Go to UniProtKB:  P55259
PHAROS:  P55259
GTEx:  ENSG00000169347 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55259
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P55259-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references