5NCE | pdb_00005nce

Structure of PsDef1 defensin from Pinus sylvestris


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

NMR structure, conformational dynamics, and biological activity of PsDef1 defensin from Pinus sylvestris.

Khairutdinov, B.I.Ermakova, E.A.Yusypovych, Y.M.Bessolicina, E.K.Tarasova, N.B.Toporkova, Y.Y.Kovaleva, V.Zuev, Y.F.Nesmelova, I.V.

(2017) Biochim Biophys Acta 1865: 1085-1094

  • DOI: https://doi.org/10.1016/j.bbapap.2017.05.012
  • Primary Citation Related Structures: 
    5NCE

  • PubMed Abstract: 

    Plants have developed a complex defense response system against pests and pathogens. Defensins, produced by plants as part of their innate immune response, form the family of small, basic, cysteine-rich proteins with activity primarily directed against fungal pathogens. In addition, plant defensins can show antibacterial activity and protease and insect amylase inhibitory activities. However, in gymnosperms, only antifungal activity of defensins has been described thus far. Here, we report antibacterial and insect α-amylase inhibition activities for defensin PsDef1 from P. sylvestris, the first defensin from gymnosperms with a broad range of biological activities described. We also report the solution NMR structure of PsDef1 and its dynamics properties assessed by a combination of experimental NMR and computational techniques. Collectively, our data provide an insight into structure, dynamics, and functional properties of PsDef1 that could be common between defensins from this taxonomic group.


  • Organizational Affiliation
    • Kazan Institute of Biochemistry and Biophysics, Lobachevsky St. 2/31, Kazan 420111, Russia; Kazan Federal University, Kremlyovskaya Str. 18, Kazan 420008, Russia.

Macromolecule Content 

  • Total Structure Weight: 5.61 kDa 
  • Atom Count: 386 
  • Modeled Residue Count: 50 
  • Deposited Residue Count: 50 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Defensin-150Pinus sylvestrisMutation(s): 0 
Gene Names: Def1
UniProt
Find proteins for A4L7R7 (Pinus sylvestris)
Explore A4L7R7 
Go to UniProtKB:  A4L7R7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4L7R7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation12-04-01286-a
Russian Foundation for Basic ResearchRussian Federation15-44-02309
Russian Foundation for Basic ResearchRussian Federation15-29-01239

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2018-05-02
    Changes: Author supporting evidence, Data collection, Experimental preparation
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary