7C0N | pdb_00007c0n

Crystal structure of a self-assembling galactosylated peptide homodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.249 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.233 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Glycopeptide Self-Assembly Modulated by Glycan Stereochemistry through Glycan-Aromatic Interactions.

He, C.Wu, S.Liu, D.Chi, C.Zhang, W.Ma, M.Lai, L.Dong, S.

(2020) J Am Chem Soc 142: 17015-17023

  • DOI: https://doi.org/10.1021/jacs.0c06360
  • Primary Citation Related Structures: 
    7C0N

  • PubMed Abstract: 

    Carbohydrates are often utilized to provide hydrophilicity and hydroxyl-based hydrogen bonds in self-assembling glycopeptides, affording versatile scaffolds with wide applicability in biomedical research. However, how stereochemistry of carbohydrates impacts the self-assembly process remains unclear. Here we have established a dimeric tyrosine-rich glycopeptide system for probing the corresponding hydrogelating behavior under the influence of site- and stereospecific glycosylations. Comparison of 18 glycoforms bearing monosaccharides at Tyr 4 and Tyr 4' shows that the glycopeptides with either α- or β-anomers exhibit contrary gelating abilities, when the glycan moieties contain axial hydroxyl groups. A high-resolution X-ray crystallographic structure of the β-galactose-containing gelator, along with other results from spectroscopic, microscopic, and rheological experiments, indicate an unusual carbohydrate-aromatic CH-π bonding that promotes glycopeptide self-assembly. These mechanistic findings, particularly evidence obtained at the angstrom scale, illuminate an unconventional role that carbohydrates can play in building supramolecules. Potential biomaterials exploiting the CH-π bond-based stabilization, as exemplified by an enzyme-resistant hydrogel, may thus be developed.

Macromolecule Content 

  • Total Structure Weight: 2 kDa 
  • Atom Count: 138 
  • Modeled Residue Count: 10 
  • Deposited Residue Count: 10 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Self-assembling galactosylated tyrosine-rich peptide
A, B
5synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.249 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.233 (DCC) 
Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.837α = 90
b = 72.837β = 90
c = 72.837γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0507602
Ministry of Science and Technology (MoST, China)China2019ZX09301-106
National Natural Science Foundation of China (NSFC)China21822701

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary