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- EMDB-38237: Cryo-EM structure of GP2 fibrils derived from human pancreas -

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Basic information

Entry
Database: EMDB / ID: EMD-38237
TitleCryo-EM structure of GP2 fibrils derived from human pancreas
Map data
Sample
  • Tissue: Surgically excised human pancreas
    • Protein or peptide: Pancreatic secretory granule membrane major glycoprotein GP2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsProtein fibril / glycoprotein / digestive tract / ANTIMICROBIAL PROTEIN
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 / innate immune response ...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 / innate immune response / external side of plasma membrane / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCao Q / Han J
Funding support China, 1 items
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, 2023-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38237.png

Downloads & links

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Map

FileDownload / File: emd_38237.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.0
Minimum - Maximum-49.063670000000002 - 62.633648000000001
Average (Standard dev.)-0.000000000002612 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38237_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38237_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Surgically excised human pancreas

EntireName: Surgically excised human pancreas
Components
  • Tissue: Surgically excised human pancreas
    • Protein or peptide: Pancreatic secretory granule membrane major glycoprotein GP2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Surgically excised human pancreas

SupramoleculeName: Surgically excised human pancreas / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pancreatic secretory granule membrane major glycoprotein GP2

MacromoleculeName: Pancreatic secretory granule membrane major glycoprotein GP2
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.533273 KDa
SequenceString: MPHLMERMVG SGLLWLALVS CILTQASAVQ RGYGNPIEAS SYGLDLDCGA PGTPEAHVCF DPCQNYTLLD EPFRSTENSA GSQGCDKNM SGWYRFVGEG GVRMSETCVQ VHRCQTDAPM WLNGTHPALG DGITNHTACA HWSGNCCFWK TEVLVKACPG G YHVYRLEG ...String:
MPHLMERMVG SGLLWLALVS CILTQASAVQ RGYGNPIEAS SYGLDLDCGA PGTPEAHVCF DPCQNYTLLD EPFRSTENSA GSQGCDKNM SGWYRFVGEG GVRMSETCVQ VHRCQTDAPM WLNGTHPALG DGITNHTACA HWSGNCCFWK TEVLVKACPG G YHVYRLEG TPWCNLRYCT VPRDPSTVED KCEKACRPEE ECLALNSTWG CFCRQDLNSS DVHSLQPQLD CGPREIKVKV DK CLLGGLG LGEEVIAYLR DPNCSSILQT EERNWVSVTS PVQASACRNI LERNQTHAIY KNTLSLVNDF IIRDTILNIN FQC AYPLDM KVSLQAALQP IVSSLNVSVD GNGEFIVRMA LFQDQNYTNP YEGDAVELSV ESVLYVGAIL EQGDTSRFNL VLRN CYATP TEDKADLVKY FIIRNSCSNQ RDSTIHVEEN GQSSESRFSV QMFMFAGHYD LVFLHCEIHL CDSLNEQCQP SCSRS QVRS EVPAIDLARV LDLGPITRRG AQSPGVMNGT PSTAGFLVAW PMVLLTVLLA WLF

UniProtKB: Pancreatic secretory granule membrane major glycoprotein GP2

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249718
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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