5NGN

Lybatide 2, a cystine-rich peptide from Lycium barbarum

  • Classification: PLANT PROTEIN
  • Organism(s): Lycium barbarum
  • Mutation(s): No 

  • Deposited: 2017-03-18 Released: 2017-07-26 
  • Deposition Author(s): Lei, J., Tan, W.L., Sakai, N., Hilgenfeld, R.
  • Funding Organization(s): German Federal Ministry of Education and Research, National Research Foundation in Singapore, NTU iFood Research Grant, NTU

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.109 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold.

Tan, W.L.Wong, K.H.Lei, J.Sakai, N.Tan, H.W.Hilgenfeld, R.Tam, J.P.

(2017) Sci Rep 7: 5194-5194

  • DOI: https://doi.org/10.1038/s41598-017-05037-1
  • Primary Citation of Related Structures:  
    5NGN

  • PubMed Abstract: 

    Cysteine-rich peptides (CRPs) of 2-6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lybatide 2
A, B, C
33Lycium barbarumMutation(s): 0 
UniProt
Find proteins for A0A2D0TC93 (Lycium barbarum)
Explore A0A2D0TC93 
Go to UniProtKB:  A0A2D0TC93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TC93
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.109 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 19.318α = 90
b = 54.655β = 100.6
c = 42.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry of Education and ResearchGermanyBMBF- 01DP12027
National Research Foundation in SingaporeSingaporeNRF-CRP8-2011-05
NTU iFood Research GrantSingaporeM4081467.080
NTUSingaporeSGP-PROG-008

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection