Crystal structure of the Plant Defensin NsD7 bound to PIP2

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Structure of the defensin NsD7 in complex with PIP2 reveals that defensin : lipid oligomer topologies are dependent on lipid type.

Jarva, M.Lay, F.T.Hulett, M.D.Kvansakul, M.

(2017) FEBS Lett 591: 2482-2490

  • DOI: https://doi.org/10.1002/1873-3468.12761
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Defensins are innate immune molecules that upon recognition of specific phospholipids can disrupt microbial membranes by forming oligomeric assemblies. Structures of two related plant defensins, NaD1 and NsD7, bound to phosphatidylinositol 4,5-bisphosphate (PIP 2 ) and phosphatidic acid (PA), respectively, revealed striking differences in their oligomeric topologies. To understand how NsD7 binds different phospholipids and rationalize the different topologies, we determined the structure of an NsD7-PIP 2 complex. This structure reveals fundamental differences in phospholipid binding compared to NsD7-PA, and an oligomeric topology nearly identical to the previously determined NaD1-PIP 2 complex, establishing that the PIP 2 fibril topology is conserved between NaD1 and NsD7. Our findings highlight the remarkable ability of defensins to bind different types of phospholipids to form oligomeric fibrils with diverse topologies.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Defensin NsD7
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, U, V, W, X
48Nicotiana suaveolensMutation(s): 0 
Find proteins for C0HK49 (Nicotiana suaveolens)
Explore C0HK49 
Go to UniProtKB:  C0HK49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0HK49
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PIO

Download Ideal Coordinates CCD File 
BA [auth B]
BB [auth S]
CA [auth C]
DB [auth T]
EA [auth D]
BA [auth B],
BB [auth S],
CA [auth C],
DB [auth T],
EA [auth D],
FB [auth U],
GA [auth E],
HA [auth F],
IA [auth G],
KA [auth H],
LA [auth I],
LB [auth V],
MB [auth W],
NA [auth J],
OA [auth K],
PA [auth L],
PB [auth X],
QA [auth M],
TA [auth N],
UA [auth O],
VA [auth P],
XA [auth Q],
Y [auth A],
ZA [auth R]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth R]
FA [auth D]
GB [auth U]
HB [auth U]
AA [auth A],
AB [auth R],
FA [auth D],
GB [auth U],
HB [auth U],
IB [auth U],
JA [auth G],
Z [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
CB [auth S]
DA [auth C]
EB [auth T]
JB [auth U]
KB [auth U]
CB [auth S],
DA [auth C],
EB [auth T],
JB [auth U],
KB [auth U],
MA [auth I],
NB [auth W],
OB [auth W],
RA [auth M],
SA [auth M],
WA [auth P],
YA [auth Q]
C3 H8 O3
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.605α = 90
b = 83.489β = 93.99
c = 105.194γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

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: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description