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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-25769 | |||||||||
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Title | Cryo-EM structure of the (TGA3)2-(NPR1)2-(TGA3)2 complex | |||||||||
![]() | Composite map | |||||||||
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![]() | NPR1 / TGA3 / Plant Immunity Complex / PLANT PROTEIN | |||||||||
Function / homology | ![]() response to herbivore / regulation of defense response to bacterium / regulation of salicylic acid mediated signaling pathway / 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 / systemic acquired resistance ...response to herbivore / regulation of defense response to bacterium / regulation of salicylic acid mediated signaling pathway / 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 / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / salicylic acid binding / plant-type hypersensitive response / response to salicylic acid / defense response to fungus / transcription coregulator activity / response to bacterium / RNA polymerase II transcription regulator complex / response to wounding / response to heat / transcription cis-regulatory region binding / calmodulin binding / response to hypoxia / nuclear body / protein ubiquitination / defense response to bacterium / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Wu Q / Zhou Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 196.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 42 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tacMC ![]() 7mk2C ![]() 7mk3C ![]() 7tadC ![]() 7taeC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Composite map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.066 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : (TGA3)2-(NPR1)2-(TGA3)2 complex
Entire | Name: (TGA3)2-(NPR1)2-(TGA3)2 complex |
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Components |
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-Supramolecule #1: (TGA3)2-(NPR1)2-(TGA3)2 complex
Supramolecule | Name: (TGA3)2-(NPR1)2-(TGA3)2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 67.886797 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPAVPRMDTT IDGFADSYEI SSTSFVATDN TDSSIVYLAA EQVLTGPDVS ALQLLSNSFE SVFDSPDDFY SDAKLVLSDG REVSFHRCV LSARSSFFKS ALAAAKKEKD SNNTAAVKLE LKEIAKDYEV GFDSVVTVLA YVYSSRVRPP PKGVSECADE N CCHVACRP ...String: GPAVPRMDTT IDGFADSYEI SSTSFVATDN TDSSIVYLAA EQVLTGPDVS ALQLLSNSFE SVFDSPDDFY SDAKLVLSDG REVSFHRCV LSARSSFFKS ALAAAKKEKD SNNTAAVKLE LKEIAKDYEV GFDSVVTVLA YVYSSRVRPP PKGVSECADE N CCHVACRP AVDFMLEVLY LAFIFKIPEL ITLYQRHLLD VVDKVVIEDT LVILKLANIC GKACMKLLDR CKEIIVKSNV DM VSLEKSL PEELVKEIID RRKELGLEVP KVKKHVSNVH KALDSDDIEL VKLLLKEDHT NLDDACALHF AVAYCNVKTA TDL LKLDLA DVNHRNPRGY TVLHVAAMRK EPQLILSLLE KGASASEATL EGRTALMIAK QATMAVECNN IPEQCKHSLK GRLC VEILE QEDKREQIPR DVPPSFAVAA DELKMTLLDL ENRVALAQRL FPTEAQAAME IAEMKGTCEF IVTSLEPDRL TGTKR TSPG VKIAPFRILE EHQSRLKALS KTVELGKRFF PRCSAVLDQI MNCEDLTQLA CGEDDTAEKR LQKKQRYMEI QETLKK AFS EDNLELGNSS LTDSTSSTSK STGGKRSNRK LSHRRRGGWS HPQFER UniProtKB: Regulatory protein NPR1 |
-Macromolecule #2: Transcription factor TGA3
Macromolecule | Name: Transcription factor TGA3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.843457 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPANNDQDED RINDKMKRRL AQNREAARKS RLRKKAHVQQ LEESRLKLSQ LEQELVRARQ QGLCVRNSSD TSYLGPAGNM NSGIAAFEM EYTHWLEEQN RRVSEIRTAL QAHIGDIELK MLVDSCLNHY ANLFRMKADA AKADVFFLMS GMWRTSTERF F QWIGGFRP ...String: GPANNDQDED RINDKMKRRL AQNREAARKS RLRKKAHVQQ LEESRLKLSQ LEQELVRARQ QGLCVRNSSD TSYLGPAGNM NSGIAAFEM EYTHWLEEQN RRVSEIRTAL QAHIGDIELK MLVDSCLNHY ANLFRMKADA AKADVFFLMS GMWRTSTERF F QWIGGFRP SELLNVVMPY VEPLTDQQLL EVRNLQQSSQ QAEEALSQGL DKLQQGLVES IAIQIKVVES VNHGAPMASA ME NLQALES FVNQADHLRQ QTLQQMSKIL TTRQAARGLL ALGEYFHRLR ALSSLWAARP REHTGGDYKD DDDKSSGYPY DVP DYA UniProtKB: Transcription factor TGA3 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 4 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.3 mg/mL |
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Buffer | pH: 7.5 Details: 25 mM HEPES pH7.5, 150 0mM NaCl, 2 mM DTT, 0.2 mM salicylic acid. |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 240 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP Details: 3 ul of the sample was applied to the grid and incubated for 60 s in the chamber set at 277.15 K and 85% humidity. The grid was blotted for 2.4 s, followed by plunge-freezing in liquid ...Details: 3 ul of the sample was applied to the grid and incubated for 60 s in the chamber set at 277.15 K and 85% humidity. The grid was blotted for 2.4 s, followed by plunge-freezing in liquid ethane cooled by liquid nitrogen.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |