6B55 | pdb_00006b55

Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid

• PDB DOI: https://doi.org/10.2210/pdb6B55/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Nicotiana alata
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-09-28 Released: 2018-05-23 
• Deposition Author(s): Jarva, M., Phan, K., Humble, C., Lay, F.T., Hulett, M., Kvansakul, M.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 29773800 
• DOI: https://doi.org/10.1038/s41467-018-04434-y
• Primary Citation Related Structures: 
  6B55


• 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.

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Organizational Affiliation: 
• Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. [e-mail].
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 20-mer - A20 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 115 kDa 
• Atom Count: 8,306 
• Modeled Residue Count: 960 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flower-specific defensin	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	48	Nicotiana alata	Mutation(s): 0
UniProt
Find proteins for Q8GTM0 (Nicotiana alata) Explore Q8GTM0  Go to UniProtKB:  Q8GTM0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PA8 (Subject of Investigation/LOI)	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]	1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE C19 H36 O8 P XYSBQYUENLDGMI-QGZVFWFLSA-M
PGE	AA [auth E], GA [auth I], HA [auth I], IA [auth J], MA [auth M]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	BA [auth G], CA [auth G], W [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	DA [auth G], KA [auth L], NA [auth O], QA [auth Q], UA [auth T]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/530

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.218	α = 90
b = 154.925	β = 90
c = 135.999	γ = 90

Software Package:

Software Name	Purpose
Aimless	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data processing
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Jarva, M., Phan, K., Humble, C., Lay, F.T., Hulett, M., Kvansakul, M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FT130101349

Revision History  

• 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
• Version 1.6: 2024-11-20
  Changes: Structure summary