+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23884 | ||||||||||||
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Title | CryoEM Structure of NPR1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information response to herbivore / regulation of salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / negative regulation of defense response / response to insect / regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / extracellular ATP signaling / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway ...response to herbivore / regulation of salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / negative regulation of defense response / response to insect / regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / extracellular ATP signaling / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / defense response to fungus / response to bacterium / response to wounding / RNA polymerase II transcription regulator complex / response to heat / response to hypoxia / protein ubiquitination / positive regulation of DNA-templated transcription / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Kumar S / Zhou Y / Dillard L / Borgnia M / Bartesaghi A / Zhou P | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23884.map.gz | 1 MB | EMDB map data format | |
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Header (meta data) | emd-23884-v30.xml emd-23884.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23884_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_23884.png | 167.1 KB | ||
Masks | emd_23884_msk_1.map | 64 MB | Mask map | |
Others | emd_23884_half_map_1.map.gz emd_23884_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23884 | HTTPS FTP |
-Related structure data
Related structure data | 7mk2MC 7mk3C 7tacC 7tadC 7taeC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23884.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39755 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23884_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_23884_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_23884_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NPR1 dimer
Entire | Name: NPR1 dimer |
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Components |
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-Supramolecule #1: NPR1 dimer
Supramolecule | Name: NPR1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Regulatory protein NPR1
Macromolecule | Name: Regulatory protein NPR1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 67.547422 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 25 mM HEPES (pH 7.5), 150 mM NaCl, 2 mM DTT |
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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |