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- PDB-6j5v: Ligand-triggered allosteric ADP release primes a plant NLR complex -

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Basic information

Entry
Database: PDB / ID: 6j5v
TitleLigand-triggered allosteric ADP release primes a plant NLR complex
Components
  • Disease resistance RPP13-like protein 4
  • Probable serine/threonine-protein kinase PBL2
  • Protein kinase superfamily protein
KeywordsPLANT 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 ...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
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 tyrosine and serine/threonine kinase ...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 tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Probable serine/threonine-protein kinase PBL2 / Disease resistance RPP13-like protein 4 / Serine/threonine-protein kinase ZRK1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 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_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Data processing / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / em_3d_reconstruction / em_ctf_correction / em_image_recording / em_software / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_reconstruction.resolution_method / _em_ctf_correction.em_image_processing_id / _em_image_recording.avg_electron_dose_per_image / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_asym.entity_id

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Structure visualization

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Assembly

Deposited unit
A: Disease resistance RPP13-like protein 4
C: Probable serine/threonine-protein kinase PBL2
B: Protein kinase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,3115
Polymers183,6633
Non-polymers6482
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5710 Å2
ΔGint-24 kcal/mol
Surface area61340 Å2

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Components

#1: 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
#2: Protein Probable serine/threonine-protein kinase PBL2 / PBS1-like protein 2 / Protein kinase 2A


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 Protein kinase superfamily protein / Protein kinase-like 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: F15B8.100, Resistance related KinaSe 1, RKS1, At3g57710
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9SVY5
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P

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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 / 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 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 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

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDName
1CTFFIND
2UCSF
3CHIMERA
4PHENIX
5RELION
6RELION
7RELION
8RELION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3342829
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.25 Å / Num. of particles: 138502 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 3TL8

3tl8

RefinementHighest resolution: 4.25 Å

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