6J5V

Ligand-triggered allosteric ADP release primes a plant NLR complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ligand-triggered allosteric ADP release primes a plant NLR complex.

Wang, J.Wang, J.Hu, M.Wu, S.Qi, J.Wang, G.Han, Z.Qi, Y.Gao, N.Wang, H.W.Zhou, J.M.Chai, J.

(2019) Science 364

  • DOI: 10.1126/science.aav5868
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The Xanthomonas campestris pv. campestris effector AvrAC uridylylates the Arabidopsis PBL2 kinase, a ...

    Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The Xanthomonas campestris pv. campestris effector AvrAC uridylylates the Arabidopsis PBL2 kinase, and the latter (PBL2 UMP ) 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 UMP in an inactive and intermediate state, respectively. The ZAR1 LRR domain, compared with animal NLR LRR domains, is differently positioned to sequester ZAR1 in an inactive state. Recognition of PBL2 UMP is exclusively through RKS1, which interacts with ZAR1 LRR PBL2 UMP 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.


    Organizational Affiliation

    Institute of Biochemistry, University of Cologne, Zuelpicher Str. 47, 50674 Cologne, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disease resistance RPP13-like protein 4A852Arabidopsis thalianaMutation(s): 0 
Gene Names: RPP13L4ZAR1At3g50950F18B3.230
Find proteins for Q38834 (Arabidopsis thaliana)
Explore Q38834 
Go to UniProtKB:  Q38834
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable serine/threonine-protein kinase PBL2C426Arabidopsis thalianaMutation(s): 0 
Gene Names: PBL2APK2AKIN1At1g14370F14L17.14
EC: 2.7.11.1
Find proteins for O49839 (Arabidopsis thaliana)
Explore O49839 
Go to UniProtKB:  O49839
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein kinase superfamily proteinB351Arabidopsis thalianaMutation(s): 0 
Gene Names: F15B8.100Resistance related KinaSe 1RKS1At3g57710ZRK1QRX3
EC: 2.7.11.1
Find proteins for Q9SVY5 (Arabidopsis thaliana)
Explore Q9SVY5 
Go to UniProtKB:  Q9SVY5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BQO
Query on BQO

Download CCD File 
C
[(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 CCD File 
C
[(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: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other