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- PDB-8xc5: Cryo-EM structure of GP2 fibrils derived from human pancreas -

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Basic information

Entry
Database: PDB / ID: 8xc5
TitleCryo-EM structure of GP2 fibrils derived from human pancreas
ComponentsPancreatic secretory granule membrane major glycoprotein GP2
KeywordsANTIMICROBIAL PROTEIN / Protein fibril / glycoprotein / digestive tract
Function / homology
Function and homology information


antigen transcytosis by M cells in mucosal-associated lymphoid tissue / zymogen granule membrane / Post-translational modification: synthesis of GPI-anchored proteins / neutrophil migration / Developmental Lineage of Pancreatic Acinar Cells / antigen binding / endosome / apical plasma membrane / membrane raft / external side of plasma membrane ...antigen transcytosis by M cells in mucosal-associated lymphoid tissue / zymogen granule membrane / Post-translational modification: synthesis of GPI-anchored proteins / neutrophil migration / Developmental Lineage of Pancreatic Acinar Cells / antigen binding / endosome / apical plasma membrane / membrane raft / external side of plasma membrane / innate immune response / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Uromodulin-like, D8C domain / : / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain ...Uromodulin-like, D8C domain / : / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Pancreatic secretory granule membrane major glycoprotein GP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCao, Q. / Han, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: PLoS Biol / Year: 2025
Title: Structure of human glycoprotein 2 reveals mechanisms underlying filament formation and adaption to proteolytic environment in the digestive tract.
Authors: Jianting Han / Meinai Song / Yijia Cheng / Wei Gong / Fei Zhang / Qin Cao /
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 ...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.
History
DepositionDec 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pancreatic secretory granule membrane major glycoprotein GP2
B: Pancreatic secretory granule membrane major glycoprotein GP2
C: Pancreatic secretory granule membrane major glycoprotein GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,4857
Polymers178,6003
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Pancreatic secretory granule membrane major glycoprotein GP2


Mass: 59533.273 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55259
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Surgically excised human pancreas / Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249718 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0073795
ELECTRON MICROSCOPYf_angle_d1.0175157
ELECTRON MICROSCOPYf_dihedral_angle_d10.861545
ELECTRON MICROSCOPYf_chiral_restr0.162623
ELECTRON MICROSCOPYf_plane_restr0.011668

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