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- PDB-6j5w: Ligand-triggered allosteric ADP release primes a plant NLR complex -

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Basic information

Entry
Database: PDB / ID: 6j5w
TitleLigand-triggered allosteric ADP release primes a plant NLR complex
Components
  • Disease resistance RPP13-like protein 4
  • RKS1
KeywordsPLANT PROTEIN / ZAR1 / RKS1
Function / homology
Function and homology information


positive regulation of defense response to bacterium / response to temperature stimulus / regulation of immune response / ADP binding / : / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity ...positive regulation of defense response to bacterium / response to temperature stimulus / regulation of immune response / ADP binding / : / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / defense response to bacterium / phosphorylation / ATP binding / nucleus / plasma membrane
Similarity search - Function
Receptor-like kinase WAK-like / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Protein kinase domain ...Receptor-like kinase WAK-like / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Disease resistance RPP13-like protein 4 / Serine/threonine-protein kinase ZRK1 / RKS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, J.Z. / Wang, J. / Hu, M.J. / Wang, H.W. / Zhou, J.M. / Chai, J.J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31421001 China
National Natural Science Foundation of China31420103906 China
CitationJournal: 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
DepositionJan 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
B: RKS1
A: Disease resistance RPP13-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7343
Polymers137,3062
Non-polymers4271
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5410 Å2
ΔGint-22 kcal/mol
Surface area49150 Å2

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Components

#1: Protein RKS1


Mass: 40142.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g57710
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: U5LSK3, UniProt: Q9SVY5*PLUS
#2: Protein Disease resistance RPP13-like protein 4 / Disease resistance protein ZAR1 / Protein HOPZ-ACTIVATED RESISTANCE 1


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
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ZAR1-RKS1 with ADP complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: YES
Source (natural)Organism: Arabidopsis (plant)
Source (recombinant)Organism: Insect cell expression vector pTIE1 (others)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 900 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
4Gctf1.18CTF correction
7UCSF Chimeramodel fitting
9PHENIX1.13model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2092456
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148718 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 3TL8

3tl8


Accession code: 3TL8 / Source name: PDB / Type: experimental model

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