Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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This is version 1.5 of the entry. See complete history


X-ray structure of a carpet-like antimicrobial defensin-phospholipid membrane disruption complex.

Jarva, M.Lay, F.T.Phan, T.K.Humble, C.Poon, I.K.H.Bleackley, M.R.Anderson, M.A.Hulett, M.D.Kvansakul, M.

(2018) Nat Commun 9: 1962-1962

  • DOI: https://doi.org/10.1038/s41467-018-04434-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Defensins are cationic antimicrobial peptides expressed throughout the plant and animal kingdoms as a first line of defense against pathogens. Membrane targeting and disruption is a crucial function of many defensins, however the precise mechanism remains unclear. Certain plant defensins form dimers that specifically bind the membrane phospholipids phosphatidic acid (PA) and phosphatidylinositol 4,5-bisphosphate, thereby triggering the assembly of defensin-lipid oligomers that permeabilize cell membranes. To understand this permeabilization mechanism, here we determine the crystal structure of the plant defensin NaD1 bound to PA. The structure reveals a 20-mer that adopts a concave sheet- or carpet-like topology where NaD1 dimers form one face and PA acyl chains form the other face of the sheet. Furthermore, we show that Arg39 is critical for PA binding, oligomerization and fungal cell killing. These findings identify a putative defensin-phospholipid membrane attack configuration that supports a longstanding proposed carpet mode of membrane disruption.

  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flower-specific defensin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
48Nicotiana alataMutation(s): 0 
Find proteins for Q8GTM0 (Nicotiana alata)
Explore Q8GTM0 
Go to UniProtKB:  Q8GTM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GTM0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PA8 (Subject of Investigation/LOI)
Query on PA8

Download Ideal Coordinates CCD File 
EA [auth H]
FA [auth I]
JA [auth L]
LA [auth M]
OA [auth P]
EA [auth H],
FA [auth I],
JA [auth L],
LA [auth M],
OA [auth P],
PA [auth Q],
RA [auth R],
SA [auth S],
TA [auth T],
U [auth A],
V [auth B],
X [auth C],
Y [auth D],
Z [auth E]
C19 H36 O8 P
Query on PGE

Download Ideal Coordinates CCD File 
AA [auth E],
GA [auth I],
HA [auth I],
IA [auth J],
MA [auth M]
C6 H14 O4
Query on PO4

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BA [auth G],
CA [auth G],
W [auth B]
O4 P
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth G],
KA [auth L],
NA [auth O],
QA [auth Q],
UA [auth T]
C2 H6 O2
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.218α = 90
b = 154.925β = 90
c = 135.999γ = 90
Software Package:
Software NamePurpose
Aimlessdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata processing
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaFT130101349

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description