5VYP | pdb_00005vyp

Crystal structure of the Plant Defensin NsD7 bound to PIP2

PDB DOI: https://doi.org/10.2210/pdb5VYP/pdb

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

Deposited: 2017-05-25 Released: 2017-08-02
Deposition Author(s): Jarva, M., Lay, F.T., Hulett, M., Kvansakul, M.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.270 (Depositor), 0.269 (DCC)
R-Value Work:
0.214 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

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

PubMed: 28741756 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12761
Primary Citation Related Structures:
5VYP

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.

Macromolecule Content

Total Structure Weight: 151.09 kDa
Atom Count: 10,341
Modeled Residue Count: 1,145
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	48	Nicotiana suaveolens	Mutation(s): 0
UniProt
Find proteins for C0HK49 (Nicotiana suaveolens) Explore C0HK49 Go to UniProtKB: C0HK49
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0HK49
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth C] SDF format, chain EA [auth D] SDF format, chain FB [auth U] SDF format, chain GA [auth E] SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain LA [auth I] SDF format, chain LB [auth V] SDF format, chain MB [auth W] SDF format, chain NA [auth J] SDF format, chain OA [auth K] SDF format, chain PA [auth L] SDF format, chain PB [auth X] SDF format, chain QA [auth M] SDF format, chain UA [auth O] SDF format, chain VA [auth P] SDF format, chain XA [auth Q] SDF format, chain Y [auth A] SDF format, chain ZA [auth R] SDF format, chain TA [auth N] SDF format, chain HA [auth F] SDF format, chain DB [auth T] SDF format, chain BB [auth S] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FB [auth U] MOL2 format, chain GA [auth E] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain LB [auth V] MOL2 format, chain MB [auth W] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain PB [auth X] MOL2 format, chain QA [auth M] MOL2 format, chain UA [auth O] MOL2 format, chain VA [auth P] MOL2 format, chain XA [auth Q] MOL2 format, chain Y [auth A] MOL2 format, chain ZA [auth R] MOL2 format, chain TA [auth N] MOL2 format, chain HA [auth F] MOL2 format, chain DB [auth T] MOL2 format, chain BB [auth S] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FB [auth U] mmCIF format, chain GA [auth E] mmCIF format, chain IA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain LB [auth V] mmCIF format, chain MB [auth W] mmCIF format, chain NA [auth J] mmCIF format, chain OA [auth K] mmCIF format, chain PA [auth L] mmCIF format, chain PB [auth X] mmCIF format, chain QA [auth M] mmCIF format, chain UA [auth O] mmCIF format, chain VA [auth P] mmCIF format, chain XA [auth Q] mmCIF format, chain Y [auth A] mmCIF format, chain ZA [auth R] mmCIF format, chain TA [auth N] mmCIF format, chain HA [auth F] mmCIF format, chain DB [auth T] mmCIF format, chain BB [auth S]	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 XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth S] Focus chain CA [auth C] Focus chain DB [auth T] Focus chain EA [auth D] Focus chain FB [auth U] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain LA [auth I] Focus chain LB [auth V] Focus chain MB [auth W] Focus chain NA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain PB [auth X] Focus chain QA [auth M] Focus chain TA [auth N] Focus chain UA [auth O] Focus chain VA [auth P] Focus chain XA [auth Q] Focus chain Y [auth A] Focus chain ZA [auth R] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth S] Focus chain CA [auth C] Focus chain DB [auth T] Focus chain EA [auth D] Focus chain FB [auth U] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain LA [auth I] Focus chain LB [auth V] Focus chain MB [auth W] Focus chain NA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain PB [auth X] Focus chain QA [auth M] Focus chain TA [auth N] Focus chain UA [auth O] Focus chain VA [auth P] Focus chain XA [auth Q] Focus chain Y [auth A] Focus chain ZA [auth R]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth R] SDF format, chain FA [auth D] SDF format, chain GB [auth U] SDF format, chain HB [auth U] SDF format, chain IB [auth U] SDF format, chain JA [auth G] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth R] MOL2 format, chain FA [auth D] MOL2 format, chain GB [auth U] MOL2 format, chain HB [auth U] MOL2 format, chain IB [auth U] MOL2 format, chain JA [auth G] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth R] mmCIF format, chain FA [auth D] mmCIF format, chain GB [auth U] mmCIF format, chain HB [auth U] mmCIF format, chain IB [auth U] mmCIF format, chain JA [auth G] mmCIF format, chain Z [auth A]	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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain AB [auth R] Focus chain FA [auth D] Focus chain GB [auth U] Focus chain HB [auth U] Focus chain IB [auth U] Focus chain JA [auth G] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth R] Focus chain FA [auth D] Focus chain GB [auth U] Focus chain HB [auth U] Focus chain IB [auth U] Focus chain JA [auth G] Focus chain Z [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CB [auth S] SDF format, chain DA [auth C] SDF format, chain EB [auth T] SDF format, chain JB [auth U] SDF format, chain KB [auth U] SDF format, chain MA [auth I] SDF format, chain NB [auth W] SDF format, chain OB [auth W] SDF format, chain RA [auth M] SDF format, chain SA [auth M] SDF format, chain WA [auth P] SDF format, chain YA [auth Q] MOL2 format, chain CB [auth S] MOL2 format, chain DA [auth C] MOL2 format, chain EB [auth T] MOL2 format, chain JB [auth U] MOL2 format, chain KB [auth U] MOL2 format, chain MA [auth I] MOL2 format, chain NB [auth W] MOL2 format, chain OB [auth W] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth M] MOL2 format, chain WA [auth P] MOL2 format, chain YA [auth Q] mmCIF format, chain CB [auth S] mmCIF format, chain DA [auth C] mmCIF format, chain EB [auth T] mmCIF format, chain JB [auth U] mmCIF format, chain KB [auth U] mmCIF format, chain MA [auth I] mmCIF format, chain NB [auth W] mmCIF format, chain OB [auth W] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth M] mmCIF format, chain WA [auth P] mmCIF format, chain YA [auth Q]	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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth S] Focus chain DA [auth C] Focus chain EB [auth T] Focus chain JB [auth U] Focus chain KB [auth U] Focus chain MA [auth I] Focus chain NB [auth W] Focus chain OB [auth W] Focus chain RA [auth M] Focus chain SA [auth M] Focus chain WA [auth P] Focus chain YA [auth Q] Interactions & Density Focus chain CB [auth S] Focus chain DA [auth C] Focus chain EB [auth T] Focus chain JB [auth U] Focus chain KB [auth U] Focus chain MA [auth I] Focus chain NB [auth W] Focus chain OB [auth W] Focus chain RA [auth M] Focus chain SA [auth M] Focus chain WA [auth P] Focus chain YA [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270 (Depositor), 0.269 (DCC)
R-Value Work: 0.214 (Depositor), 0.216 (DCC)
R-Value Observed: 0.217 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.605	α = 90
b = 83.489	β = 93.99
c = 105.194	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

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

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
Version 1.5: 2024-11-20
Changes: Structure summary