9KAP | pdb_00009kap

Cryo-EM structure of glycopeptide fibril


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and Structural Elucidation of Glycopeptide Fibrils: Emulating Glycosaminoglycan Functions for Biomedical Applications.

Xia, W.Xu, Z.Dong, H.Zhang, S.He, C.Li, D.Sun, B.Dai, B.Dong, S.Liu, C.

(2025) J Am Chem Soc 147: 20132-20143

  • DOI: https://doi.org/10.1021/jacs.5c07039
  • Primary Citation of Related Structures:  
    9KAP

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Interdisciplinary Research Center on Biology and Chemistry, State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYR-TYR-CYS-TYR-TYR5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDP (Subject of Investigation/LOI)
Query on BDP

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth E]
P [auth F]
Q [auth I]
M [auth A],
N [auth B],
O [auth E],
P [auth F],
Q [auth I],
R [auth J],
S [auth M],
T [auth N],
U [auth Q],
V [auth R],
W [auth U],
X [auth V]
beta-D-glucopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references