6J6I

Reconstitution and structure of a plant NLR resistosome conferring immunity


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Reconstitution and structure of a plant NLR resistosome conferring immunity.

Wang, J.Hu, M.Wang, J.Qi, J.Han, Z.Wang, G.Qi, Y.Wang, H.W.Zhou, J.M.Chai, J.

(2019) Science 364: --

  • DOI: 10.1126/science.aav5870
  • Primary Citation of Related Structures:  

  • PubMed 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 understood. We reconstituted an active complex conta ...

    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 Arabidopsis 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.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.,Institute of Biochemistry, University of Cologne, Zuelpicher Strasse 47, 50674 Cologne, Germany.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China.,Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.,Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K.,Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wfeng@ibp.ac.cn.,Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA.,the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Electronic address: ckerfeld@lbl.gov.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. jysuh@snu.ac.kr.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Medicinal Chemistry, Department of Internal Medicine, Comprehensive Cancer Center, and Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland. Electronic address: mbretner@ch.pw.edu.pl.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. chengzh@pitt.edu.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.,Department of Biochemistry & Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA williamsrs@niehs.nih.gov.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Sorbonne Université, Collège doctoral, 75005, Paris, France.,Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia. Electronic address: r.mcgeary@uq.edu.au.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K. jworrall@essex.ac.uk.,State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Drug Discovery Group Cancer Research UK Manchester Institute, Manchester, UK.,the Departments of Life Sciences and.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K. c.dong@uea.ac.uk.,D. E. Shaw Research, New York, NY, USA.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.,Large Scale Structures Group, Institut Laue-Langevin, Grenoble Cedex 9, 38042, France.,Structural Biology Research Center, VIB, Brussels, Belgium.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.,the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan.,Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Shanghai Institute of Precision Medicine, Shanghai 200125, China.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan. jysuh@snu.ac.kr.,Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China.,Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, 02792, Korea.,Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia; Helwan University, Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan, Egypt.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria, christian.obinger@boku.ac.at.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and.,Dropbox, New York, NY, USA.,Bioss Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia.,Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, wipa@sut.ac.th.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France. jacqueline.cherfils@ens-paris-saclay.fr.,Biomedical Sciences, Defence Science and Technology Laboratory Porton Down, SP4 0JQ Salisbury, United Kingdom.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,Max Planck Institute for Plant Breeding Research, Cologne, Germany.,the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium.,Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable serine/threonine-protein kinase PBL2
A
426Arabidopsis thalianaMutation(s): 0 
Gene Names: PBL2 (APK2A, KIN1)
EC: 2.7.11.1
Find proteins for O49839 (Arabidopsis thaliana)
Go to UniProtKB:  O49839
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein kinase superfamily protein
B
351Arabidopsis thalianaMutation(s): 0 
Gene Names: F15B8.100 (Resistance related KinaSe 1, RKS1)
Find proteins for Q9SVY5 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SVY5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Disease resistance RPP13-like protein 4
C, F, G, L, O
852Arabidopsis thalianaMutation(s): 0 
Gene Names: RPP13L4 (ZAR1)
Find proteins for Q38834 (Arabidopsis thaliana)
Go to UniProtKB:  Q38834
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
C, F, G, L, O
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
BQO
Query on BQO

Download SDF File 
Download CCD File 
A
[(2~{R},3~{S})-3-azanyl-4-oxidanylidene-butan-2-yl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C13 H20 N3 O10 P
MTUPUTQZEYXVLI-ZXIMEAKPSA-N
 Ligand Interaction
BQL
Query on BQL

Download SDF File 
Download CCD File 
A
[(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C12 H18 N3 O10 P
DGKQNNIXYUXPCL-JBSYKWBFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31421001
National Natural Science Foundation of ChinaChina31420103906

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references, Structure summary