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- EMDB-62213: Cryo-EM structure of glycopeptide fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-62213
TitleCryo-EM structure of glycopeptide fibril
Map data
Sample
  • Cell: Cryo-EM structure of glycopeptide fibril
    • Protein or peptide: TYR-TYR-CYS-TYR-TYR
  • Ligand: beta-D-glucopyranuronic acid
Keywordshelical fibril / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXia WC / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Am Chem Soc / Year: 2025
Title: Design and Structural Elucidation of Glycopeptide Fibrils: Emulating Glycosaminoglycan Functions for Biomedical Applications.
Authors: Wencheng Xia / Zhongxin Xu / Hui Dong / Shengnan Zhang / Changdong He / Dan Li / Bo Sun / Bin Dai / Suwei Dong / Cong Liu /
Abstract: Glycosaminoglycans (GAGs) are essential polysaccharides crucial for various cellular functions, such as cell proliferation, migration, and differentiation. However, their complex structure and ...Glycosaminoglycans (GAGs) are essential polysaccharides crucial for various cellular functions, such as cell proliferation, migration, and differentiation. However, their complex structure and variability from natural sources pose challenges for functional studies and therapeutic applications. In this study, we engineered a glycopeptide that assembles into fibrils, emulating the functional attributes of GAGs. Utilizing cryo-EM, we elucidated the atomic structure of the designed glycopeptide fibril, which is composed of three identical protofilaments intertwined into a left-handed helix and held together by a variety of intermolecular interactions. Remarkably, the functional sugar units, glucuronic acids, are orderly positioned on the fibril surface, making them readily accessible to the solvent. This distinctive spatial configuration allows the designed glycopeptide fibril to effectively mimic key GAG functionalities, including the promotion of cell proliferation, cell migration, and osteogenic differentiation. Our findings offer a structural framework for designing glycan functionalities on glycopeptide fibrils and open avenues for developing glycopeptide-based materials with versatile biological activities. This work further enhances the potential of these materials for applications in therapeutic and regenerative medicine.
History
DepositionOct 29, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62213.png

Downloads & links

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Map

FileDownload / File: emd_62213.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 180 pix.
= 190.8 Å		1.06 Å/pix.
x 180 pix.
= 190.8 Å		1.06 Å/pix.
x 180 pix.
= 190.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.23450205 - 0.3432059
Average (Standard dev.)0.00044962534 (±0.008899653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 190.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62213_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62213_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of glycopeptide fibril

EntireName: Cryo-EM structure of glycopeptide fibril
Components
  • Cell: Cryo-EM structure of glycopeptide fibril
    • Protein or peptide: TYR-TYR-CYS-TYR-TYR
  • Ligand: beta-D-glucopyranuronic acid

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Supramolecule #1: Cryo-EM structure of glycopeptide fibril

SupramoleculeName: Cryo-EM structure of glycopeptide fibril / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: TYR-TYR-CYS-TYR-TYR

MacromoleculeName: TYR-TYR-CYS-TYR-TYR / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 773.853 Da
SequenceString:
YYCYY

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Macromolecule #2: beta-D-glucopyranuronic acid

MacromoleculeName: beta-D-glucopyranuronic acid / type: ligand / ID: 2 / Number of copies: 12 / Formula: BDP
Molecular weightTheoretical: 194.139 Da
Chemical component information

ChemComp-BDP:
beta-D-glucopyranuronic acid

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.19 Å
Applied symmetry - Helical parameters - Δ&Phi: 115.10 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 693071
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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