7CKE | pdb_00007cke

Solution structure of NCR169 oxidized form 2 from Medicago truncatula


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 7CKE

This is version 1.2 of the entry. See complete history

Literature

Structure and antimicrobial activity of NCR169, a nodule-specific cysteine-rich peptide of Medicago truncatula.

Isozumi, N.Masubuchi, Y.Imamura, T.Mori, M.Koga, H.Ohki, S.

(2021) Sci Rep 11: 9923-9923

  • DOI: https://doi.org/10.1038/s41598-021-89485-w
  • Primary Citation Related Structures: 
    7CKD, 7CKE

  • PubMed Abstract: 

    A model legume, Medicago truncatula, has over 600 nodule-specific cysteine-rich (NCR) peptides required for symbiosis with rhizobia. Among them, NCR169, an essential factor for establishing symbiosis, has four cysteine residues that are indispensable for its function. However, knowledge of NCR169 structure and mechanism of action is still lacking. In this study, we solved two NMR structures of NCR169 caused by different disulfide linkage patterns. We show that both structures have a consensus C-terminal β-sheet attached to an extended N-terminal region with dissimilar features; one moves widely, whereas the other is relatively stapled. We further revealed that the disulfide bonds of NCR169 contribute to its structural stability and solubility. Regarding the function, one of the NCR169 oxidized forms could bind to negatively charged bacterial phospholipids. Furthermore, the positively charged lysine-rich region of NCR169 may be responsible for its antimicrobial activity against Escherichia coli and Sinorhizobium meliloti. This active region was disordered even in the phospholipid bound state, suggesting that the disordered conformation of this region is key to its function. Morphological observations suggested the mechanism of action of NCR169 on bacteria. The present study on NCR169 provides new insights into the structure and function of NCR peptides.


  • Organizational Affiliation
    • Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan.

Macromolecule Content 

  • Total Structure Weight: 4.63 kDa 
  • Atom Count: 323 
  • Modeled Residue Count: 39 
  • Deposited Residue Count: 39 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nodule Cysteine-Rich (NCR) secreted peptide39Medicago truncatulaMutation(s): 0 
Gene Names: MTR_7g029760
UniProt
Find proteins for A7KHA7 (Medicago truncatula)
Explore A7KHA7 
Go to UniProtKB:  A7KHA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7KHA7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references, Other
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary