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- PDB-6j5t: Reconstitution and structure of a plant NLR resistosome conferrin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j5t | |||||||||
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Title | Reconstitution and structure of a plant NLR resistosome conferring immunity | |||||||||
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![]() | PLANT PROTEIN / resistosome | |||||||||
Function / homology | ![]() positive regulation of defense response to bacterium / Tat protein binding / response to temperature stimulus / regulation of immune response / ADP binding / defense response / : / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway ...positive regulation of defense response to bacterium / Tat protein binding / response to temperature stimulus / regulation of immune response / ADP binding / defense response / : / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / defense response to bacterium / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wang, J.Z. / Wang, J. / Hu, M.J. / Wang, H.W. / Zhou, J.M. / Chai, J.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Reconstitution and structure of a plant NLR resistosome conferring immunity. Authors: Jizong Wang / Meijuan Hu / Jia Wang / Jinfeng Qi / Zhifu Han / Guoxun Wang / Yijun Qi / Hong-Wei Wang / Jian-Min Zhou / Jijie Chai / ![]() ![]() Abstract: Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. Biochemical mechanisms underlying plant NLR activation have until now remained poorly ...Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. Biochemical mechanisms underlying plant NLR activation have until now remained poorly understood. We reconstituted an active complex containing the coiled-coil NLR ZAR1, the pseudokinase RKS1, uridylated protein kinase PBL2, and 2'-deoxyadenosine 5'-triphosphate (dATP), demonstrating the oligomerization of the complex during immune activation. The cryo-electron microscopy structure reveals a wheel-like pentameric ZAR1 resistosome. Besides the nucleotide-binding domain, the coiled-coil domain of ZAR1 also contributes to resistosome pentamerization by forming an α-helical barrel that interacts with the leucine-rich repeat and winged-helix domains. Structural remodeling and fold switching during activation release the very N-terminal amphipathic α helix of ZAR1 to form a funnel-shaped structure that is required for the plasma membrane association, cell death triggering, and disease resistance, offering clues to the biochemical function of a plant resistosome. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 960.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 171.3 KB | Display | |
Data in CIF | ![]() | 257.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0680MC ![]() 0688C ![]() 6j6iC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 46356.430 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O49839*PLUS, non-specific serine/threonine protein kinase #2: Protein | Mass: 40142.375 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: F15B8.100, Resistance related KinaSe 1, RKS1, At3g57710 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9SVY5 #3: Protein | Mass: 97163.977 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q38834 #4: Chemical | ChemComp-U5P / #5: Chemical | ChemComp-DTP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: resistosome / Type: COMPLEX / Entity ID: #2-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.13 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: Insect cell expression vector pTIE1 (others) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 900 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Particle selection | Num. of particles selected: 2092456 | ||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Num. of particles: 196707 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||
Atomic model building | PDB-ID: 3TL8 | ||||||||||||||||||
Refinement | Highest resolution: 3.4 Å |