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- EMDB-23884: CryoEM Structure of NPR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-23884
TitleCryoEM Structure of NPR1
Map data
Sample
  • Complex: NPR1 dimer
    • Protein or peptide: Regulatory protein NPR1
  • Ligand: ZINC ION
KeywordsNPR1 / SAR / plant immunity / PLANT PROTEIN / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of salicylic acid mediated signaling pathway / regulation of defense response to bacterium / response to herbivore / regulation of systemic acquired resistance / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / extracellular ATP signaling / response to insect / salicylic acid binding ...regulation of salicylic acid mediated signaling pathway / regulation of defense response to bacterium / response to herbivore / regulation of systemic acquired resistance / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / extracellular ATP signaling / response to insect / salicylic acid binding / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to salicylic acid / defense response to fungus / response to bacterium / transcription coregulator activity / response to wounding / RNA polymerase II transcription regulator complex / response to heat / nuclear body / response to hypoxia / defense response to bacterium / protein ubiquitination / positive regulation of DNA-templated transcription / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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 / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily ...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 / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Regulatory protein NPR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKumar S / Zhou Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)115355 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118036 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2022
Title: Structural basis of NPR1 in activating plant immunity.
Authors: Shivesh Kumar / Raul Zavaliev / Qinglin Wu / Ye Zhou / Jie Cheng / Lucas Dillard / Jordan Powers / John Withers / Jinshi Zhao / Ziqiang Guan / Mario J Borgnia / Alberto Bartesaghi / Xinnian Dong / Pei Zhou /
Abstract: NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid. Despite the important role of NPR1 in plant immunity, understanding of its regulatory ...NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid. Despite the important role of NPR1 in plant immunity, understanding of its regulatory mechanisms has been hindered by a lack of structural information. Here we report cryo-electron microscopy and crystal structures of Arabidopsis NPR1 and its complex with the transcription factor TGA3. Cryo-electron microscopy analysis reveals that NPR1 is a bird-shaped homodimer comprising a central Broad-complex, Tramtrack and Bric-à-brac (BTB) domain, a BTB and carboxyterminal Kelch helix bundle, four ankyrin repeats and a disordered salicylic-acid-binding domain. Crystal structure analysis reveals a unique zinc-finger motif in BTB for interacting with ankyrin repeats and mediating NPR1 oligomerization. We found that, after stimulation, salicylic-acid-induced folding and docking of the salicylic-acid-binding domain onto ankyrin repeats is required for the transcriptional cofactor activity of NPR1, providing a structural explanation for a direct role of salicylic acid in regulating NPR1-dependent gene expression. Moreover, our structure of the TGA3-NPR1-TGA3 complex, DNA-binding assay and genetic data show that dimeric NPR1 activates transcription by bridging two fatty-acid-bound TGA3 dimers to form an enhanceosome. The stepwise assembly of the NPR1-TGA complex suggests possible hetero-oligomeric complex formation with other transcription factors, revealing how NPR1 reprograms the defence transcriptome.
History
DepositionApr 21, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
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  • Surface view with fitted model
  • Atomic models: PDB-7mk2
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_23884.png

Downloads & links

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Map

FileDownload / File: emd_23884.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 256 pix.
= 357.773 Å		1.4 Å/pix.
x 256 pix.
= 357.773 Å		1.4 Å/pix.
x 256 pix.
= 357.773 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39755 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.5
Minimum - Maximum-1.8888273 - 3.5156786
Average (Standard dev.)-0.000000000000005 (±0.033728972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 357.7728 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.397550781251.397550781251.39755078125
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z357.773357.773357.773
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-160
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.8893.516-0.000

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Supplemental data

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Mask #1

Fileemd_23884_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_23884_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_23884_half_map_2.map
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Sample components

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Entire : NPR1 dimer

EntireName: NPR1 dimer
Components
  • Complex: NPR1 dimer
    • Protein or peptide: Regulatory protein NPR1
  • Ligand: ZINC ION

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Supramolecule #1: NPR1 dimer

SupramoleculeName: NPR1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Regulatory protein NPR1

MacromoleculeName: Regulatory protein NPR1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 67.547422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPLMDTTIDG FADSYEISST SFVATDNTDS SIVYLAAEQV LTGPDVSALQ LLSNSFESVF DSPDDFYSDA KLVLSDGREV SFHRCVLSA RSSFFKSALA AAKKEKDSNN TAAVKLELKE IAKDYEVGFD SVVTVLAYVY SSRVRPPPKG VSECADENCC H VACRPAVD ...String:
GPLMDTTIDG FADSYEISST SFVATDNTDS SIVYLAAEQV LTGPDVSALQ LLSNSFESVF DSPDDFYSDA KLVLSDGREV SFHRCVLSA RSSFFKSALA AAKKEKDSNN TAAVKLELKE IAKDYEVGFD SVVTVLAYVY SSRVRPPPKG VSECADENCC H VACRPAVD FMLEVLYLAF IFKIPELITL YQRHLLDVVD KVVIEDTLVI LKLANICGKA CMKLLDRCKE IIVKSNVDMV SL EKSLPEE LVKEIIDRRK ELGLEVPKVK KHVSNVHKAL DSDDIELVKL LLKEDHTNLD DACALHFAVA YCNVKTATDL LKL DLADVN HRNPRGYTVL HVAAMRKEPQ LILSLLEKGA SASEATLEGR TALMIAKQAT MAVECNNIPE QCKHSLKGRL CVEI LEQED KREQIPRDVP PSFAVAADEL KMTLLDLENR VALAQRLFPT EAQAAMEIAE MKGTCEFIVT SLEPDRLTGT KRTSP GVKI APFRILEEHQ SRLKALSKTV ELGKRFFPRC SAVLDQIMNC EDLTQLACGE DDTAEKRLQK KQRYMEIQET LKKAFS EDN LELGNSSLTD STSSTSKSTG GKRSNRKLSH RRRGGWSHPQ FEK

UniProtKB: Regulatory protein NPR1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 25 mM HEPES (pH 7.5), 150 mM NaCl, 2 mM DTT
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75705
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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