1AYJ

DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Determination of the three-dimensional solution structure of Raphanus sativus antifungal protein 1 by 1H NMR.

Fant, F.Vranken, W.Broekaert, W.Borremans, F.

(1998) J.Mol.Biol. 279: 257-270

  • DOI: 10.1006/jmbi.1998.1767

  • PubMed Abstract: 
  • Raphanus sativus Antifungal Protein 1 (Rs-AFP1) is a 51 amino acid residue plant defensin isolated from radish (Raphanus sativus L.) seeds. The three-dimensional structure in aqueous solution has been determined from two-dimensional 1H NMR data recor ...

    Raphanus sativus Antifungal Protein 1 (Rs-AFP1) is a 51 amino acid residue plant defensin isolated from radish (Raphanus sativus L.) seeds. The three-dimensional structure in aqueous solution has been determined from two-dimensional 1H NMR data recorded at 500 MHz using the DIANA/REDAC calculation protocols. Experimental constraints consisted of 787 interproton distances extracted from NOE cross-peaks, 89 torsional constraints from 106 vicinal interproton coupling constants and 32 stereospecific assignments of prochiral protons. Further refinement by simulated annealing resulted in a set of 20 structures having pairwise root-mean-square differences of 1.35(+/- 0.35) A over the backbone heavy atoms and 2.11(+/- 0.46) A over all heavy atoms. The molecule adopts a compact globular fold comprising an alpha-helix from Asn18 till Leu28 and a triple-stranded beta-sheet (beta 1 = Lys2-Arg6, beta 2 = His33-Tyr38 and beta 3 = His43-Pro50). The central strand of this beta-sheet is connected by two disulfide bridges (Cys21-Cys45 and Cys25-Cys47) to the alpha-helix. The connection between beta-strand 2 and 3 is formed by a type VIa beta-turn. Even the loop (Pro7 to Asn17) between beta-strand 1 and the alpha-helix is relatively well defined. The structure of Raphanus sativus Antifungal Protein 1 features all the characteristics of the "cysteine stabilized alpha beta motif". A comparison of the complete structure and of the regions important for interaction with the fungal receptor according to a mutational study, is made with the structure of gamma-thionin, a plant defensin that has no antifungal activity. It is concluded that this interaction is both electrostatic and specific, and some possible scenarios for the mode of action are given.


    Related Citations: 
    • Solution Conformation of Raphanus Sativus Antifungal Protein 1 (Rs-Afp1) by 1H Nuclear Magnetic Resonance. Resonance Assignments, Secondary Structure and Global Fold
      Fant, F.,Vranken, W.F.,Martins, J.C.,Borremans, F.A.M.
      (1997) Bull.Soc.Chim.Belg. 106: 51


    Organizational Affiliation

    Department of Organic Chemistry, University of Gent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIFUNGAL PROTEIN 1
A
51Raphanus sativusMutation(s): 0 
Gene Names: AFP1
Find proteins for P69241 (Raphanus sativus)
Go to UniProtKB:  P69241
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND ENERGY 
  • Olderado: 1AYJ Olderado
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other