7MK2

CryoEM Structure of NPR1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis of NPR1 in activating plant immunity.

Kumar, S.Zavaliev, R.Wu, Q.Zhou, Y.Cheng, J.Dillard, L.Powers, J.Withers, J.Zhao, J.Guan, Z.Borgnia, M.J.Bartesaghi, A.Dong, X.Zhou, P.

(2022) Nature 605: 561-566

  • DOI: https://doi.org/10.1038/s41586-022-04699-w
  • Primary Citation of Related Structures:  
    7MK2, 7MK3, 7TAC, 7TAD, 7TAE

  • PubMed Abstract: 

    NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid 1-4 . Despite the important role of NPR1 in plant immunity 5-7 , understanding of its regulatory mechanisms has been hindered by a lack of structural information. Here we report cryo-electron microscopy and crystal structures of Arabidopsis NPR1 and its complex with the transcription factor TGA3. Cryo-electron microscopy analysis reveals that NPR1 is a bird-shaped homodimer comprising a central Broad-complex, Tramtrack and Bric-à-brac (BTB) domain, a BTB and carboxyterminal Kelch helix bundle, four ankyrin repeats and a disordered salicylic-acid-binding domain. Crystal structure analysis reveals a unique zinc-finger motif in BTB for interacting with ankyrin repeats and mediating NPR1 oligomerization. We found that, after stimulation, salicylic-acid-induced folding and docking of the salicylic-acid-binding domain onto ankyrin repeats is required for the transcriptional cofactor activity of NPR1, providing a structural explanation for a direct role of salicylic acid in regulating NPR1-dependent gene expression. Moreover, our structure of the TGA3 2 -NPR1 2 -TGA3 2 complex, DNA-binding assay and genetic data show that dimeric NPR1 activates transcription by bridging two fatty-acid-bound TGA3 dimers to form an enhanceosome. The stepwise assembly of the NPR1-TGA complex suggests possible hetero-oligomeric complex formation with other transcription factors, revealing how NPR1 reprograms the defence transcriptome.


  • Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein NPR1
A, B
606Arabidopsis thalianaMutation(s): 0 
Gene Names: NPR1NIM1SAI1At1g64280F15H21.6
UniProt
Find proteins for P93002 (Arabidopsis thaliana)
Explore P93002 
Go to UniProtKB:  P93002
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93002
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States115355
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States118036
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2022-06-01
    Changes: Database references
  • Version 1.4: 2022-06-22
    Changes: Database references
  • Version 1.5: 2024-05-29
    Changes: Data collection