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Yorodumi- PDB-6j5u: Ligand-triggered allosteric ADP release primes a plant NLR complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j5u | |||||||||
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Title | Ligand-triggered allosteric ADP release primes a plant NLR complex | |||||||||
Components |
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Keywords | PLANT PROTEIN / ZAR1 / RKS1 / PBL2-UMP | |||||||||
Function / homology | Function and homology information 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 ...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 / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wang, J.Z. / Wang, J. / Meijuan, H. / Wang, H.W. / Zhou, J.M. / Chai, J.J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Science / Year: 2019 Title: Ligand-triggered allosteric ADP release primes a plant NLR complex. Authors: Jizong Wang / Jia Wang / Meijuan Hu / Shan Wu / Jinfeng Qi / Guoxun Wang / Zhifu Han / Yijun Qi / Ning Gao / Hong-Wei Wang / Jian-Min Zhou / Jijie Chai / Abstract: Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The pv. effector AvrAC uridylylates the PBL2 kinase, and the latter (PBL2) ...Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The pv. effector AvrAC uridylylates the PBL2 kinase, and the latter (PBL2) acts as a ligand to activate the NLR ZAR1 precomplexed with the RKS1 pseudokinase. Here we report the cryo-electron microscopy structures of ZAR1-RKS1 and ZAR1-RKS1-PBL2 in an inactive and intermediate state, respectively. The ZAR1 domain, compared with animal NLR domains, is differently positioned to sequester ZAR1 in an inactive state. Recognition of PBL2 is exclusively through RKS1, which interacts with ZAR1 PBL2 binding stabilizes the RKS1 activation segment, which sterically blocks ZAR1 adenosine diphosphate (ADP) binding. This engenders a more flexible NB domain without conformational changes in the other ZAR1 domains. Our study provides a structural template for understanding plant NLRs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6j5u.cif.gz | 221.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j5u.ent.gz | 173.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j5u_validation.pdf.gz | 872.4 KB | Display | wwPDB validaton report |
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Full document | 6j5u_full_validation.pdf.gz | 916.4 KB | Display | |
Data in XML | 6j5u_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 6j5u_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/6j5u ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j5u | HTTPS FTP |
-Related structure data
Related structure data | 0681MC 0682C 0683C 6j5vC 6j5wC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 97163.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RPP13L4, ZAR1, At3g50950, F18B3.230 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q38834 |
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#2: Protein | Mass: 46356.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PBL2, APK2A, KIN1, At1g14370, F14L17.14 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O49839, non-specific serine/threonine protein kinase |
#3: Protein | Mass: 40142.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) Gene: F15B8.100, Resistance related KinaSe 1, RKS1, At3g57710 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9SVY5 |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ZAR1-RKS1 with ADP complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.13 MDa / Experimental value: YES |
Source (natural) | Organism: Arabidopsis (plant) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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: 3342829 | ||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Num. of particles: 404311 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||
Atomic model building | PDB-ID: 3TL8 | ||||||||||||||||||
Refinement | Highest resolution: 3.9 Å |