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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 / 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 / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain ...Uromodulin-like, D8C domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / 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: Cao Q / Han J
History
DepositionDec 8, 2023-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 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

Projections

Slices (1/2)
Density Histograms

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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