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- PDB-9zjn: Cryo-EM structure of the Arabidopsis salicylic acid-bound NPR1-ME... -

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Basic information

Entry
Database: PDB / ID: 9zjn
TitleCryo-EM structure of the Arabidopsis salicylic acid-bound NPR1-MED15 complex
Components
  • Mediator of RNA polymerase II transcription subunit 15a
  • Regulatory protein NPR1
KeywordsPLANT PROTEIN / NPR1 / MED15 / salicylic acid / SA receptor / mediator / plant immunity / Arabidopsis
Function / homology
Function and homology information


induced systemic resistance / regulation of salicylic acid mediated signaling pathway / regulation of defense response to bacterium / regulation of systemic acquired resistance / extracellular ATP signaling / regulation of jasmonic acid mediated signaling pathway / response to insect / negative regulation of defense response / systemic acquired resistance, salicylic acid mediated signaling pathway / salicylic acid binding ...induced systemic resistance / regulation of salicylic acid mediated signaling pathway / regulation of defense response to bacterium / regulation of systemic acquired resistance / extracellular ATP signaling / regulation of jasmonic acid mediated signaling pathway / response to insect / negative regulation of defense response / systemic acquired resistance, salicylic acid mediated signaling pathway / salicylic acid binding / response to salicylic acid / systemic acquired resistance / plant-type hypersensitive response / positive regulation of fatty acid biosynthetic process / mediator complex / defense response to fungus / response to bacterium / transcription coregulator activity / response to wounding / chromatin DNA binding / response to heat / response to hypoxia / nuclear body / transcription coactivator activity / defense response to bacterium / protein ubiquitination / positive regulation of DNA-templated transcription / DNA-templated transcription / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 15a/b/c-like / : / Zinc finger C2HC NPR-type profile. / NPR1/NIM1-like, C-terminal / Regulatory protein NPR, central domain / Regulatory protein NPR / Domain of unknown function (DUF3420) / NPR1/NIM1 like defence protein C terminal / Mediator complex subunit 15, KIX domain / KIX domain ...Mediator of RNA polymerase II transcription subunit 15a/b/c-like / : / Zinc finger C2HC NPR-type profile. / NPR1/NIM1-like, C-terminal / Regulatory protein NPR, central domain / Regulatory protein NPR / Domain of unknown function (DUF3420) / NPR1/NIM1 like defence protein C terminal / Mediator complex subunit 15, KIX domain / KIX domain / : / ARC105/Med15 mediator subunit C-terminal domain / Coactivator CBP, KIX domain superfamily / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Mediator of RNA polymerase II transcription subunit 15a / Regulatory protein NPR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, S. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis salicylic acid-bound NPR1-MED15 complex
Authors: Zhang, S. / Zheng, N.
History
DepositionDec 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein NPR1
B: Regulatory protein NPR1
C: Mediator of RNA polymerase II transcription subunit 15a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2526
Polymers126,9833
Non-polymers2693
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Regulatory protein NPR1 / BTB/POZ domain-containing protein NPR1 / Non-inducible immunity protein 1 / Nim1 / Nonexpresser of ...BTB/POZ domain-containing protein NPR1 / Non-inducible immunity protein 1 / Nim1 / Nonexpresser of PR genes 1 / Salicylic acid insensitive 1 / Sai1


Mass: 58778.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A near full-length version of NPR1 (amino acids 40-564) was used in this study.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NPR1, NIM1, SAI1, At1g64280, F15H21.6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P93002
#2: Protein Mediator of RNA polymerase II transcription subunit 15a


Mass: 9424.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MED15A KIX domain (aa 17-98) was used in this study.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MED15A, MED15_2, At1g15780, F7H2.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4I171
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of dimeric NPR1 with salicylic acid and MED15A KIX domain
Type: COMPLEX
Details: A near full-length version of NPR1 was co-expressed in E. coli and purified with MED15A KIX domain in presence of SA through gravity affinity purification. Fusion protein tags were cleaved ...Details: A near full-length version of NPR1 was co-expressed in E. coli and purified with MED15A KIX domain in presence of SA through gravity affinity purification. Fusion protein tags were cleaved by TEV enzyme. Purified tag-free NPR1-MED15A KIX-SA complex was cross-linked with BS3, further purified with gel filtration and loaded on ANT grids for Cryo-EM.
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.13645 MDa / Experimental value: YES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.5
Details: 150 mM NaCl, 20 mM HEPES pH 7.5, 0.5 mM TCEP, 0.1% DM detergent
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
30.5 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was cross-linked with BS3 and mixed with 0.1% DM detergent prior to being loaded on grids. Due to the presence of the detergent, high concentration of the sample was required to ...Details: The sample was cross-linked with BS3 and mixed with 0.1% DM detergent prior to being loaded on grids. Due to the presence of the detergent, high concentration of the sample was required to get a desired distribution of particles.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K
Details: Sample was manually applied to grid and blotted outside of the Vitrobot twice before being applied once and two-side blotted with two layers of blotting papers with blot force 0 for 9 ...Details: Sample was manually applied to grid and blotted outside of the Vitrobot twice before being applied once and two-side blotted with two layers of blotting papers with blot force 0 for 9 seconds within the Vitrobot chamber. Grids used: Amorphous Ni-Titanium Holey Foil Grids from Molecular Dimensions; Gold support grid, Ni-Ti holey foil, 300 mesh, 1.2/1.3 Aperture Pitch

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 7 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 773558 / Symmetry type: POINT

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