7L7W | pdb_00007l7w

Crystal structure of Arabidopsis NRG1.1 CC-R domain K94E/K96E mutant

• PDB DOI: https://doi.org/10.2210/pdb7L7W/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-30 Released: 2021-06-16 
• Deposition Author(s): Walton, W.G., Wan, L., Lietzan, A.D., Redinbo, M.R., Dangl, J.L.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Plant "helper" immune receptors are Ca 2+ -permeable nonselective cation channels.

Jacob, P., Kim, N.H., Wu, F., El-Kasmi, F., Chi, Y., Walton, W.G., Furzer, O.J., Lietzan, A.D., Sunil, S., Kempthorn, K., Redinbo, M.R., Pei, Z.M., Wan, L., Dangl, J.L.

(2021) Science 373: 420-425

• PubMed: 34140391 
• DOI: https://doi.org/10.1126/science.abg7917
• Primary Citation Related Structures: 
  7L7V, 7L7W


• PubMed Abstract: 
  

  Plant nucleotide-binding leucine-rich repeat receptors (NLRs) regulate immunity and cell death. In Arabidopsis , a subfamily of "helper" NLRs is required by many "sensor" NLRs. Active NRG1.1 oligomerized, was enriched in plasma membrane puncta, and conferred cytoplasmic calcium ion (Ca ²⁺ ) influx in plant and human cells. NRG1.1-dependent Ca ²⁺ influx and cell death were sensitive to Ca ²⁺ channel blockers and were suppressed by mutations affecting oligomerization or plasma membrane enrichment. Ca ²⁺ influx and cell death mediated by NRG1.1 and ACTIVATED DISEASE RESISTANCE 1 (ADR1), another helper NLR, required conserved negatively charged N-terminal residues. Whole-cell voltage-clamp recordings demonstrated that Arabidopsis helper NLRs form Ca ²⁺ -permeable cation channels to directly regulate cytoplasmic Ca ²⁺ levels and consequent cell death. Thus, helper NLRs transduce cell death signals directly.

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Organizational Affiliation: 
• Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Biology, Duke University, Durham, NC 27708, USA.
Department of Horticulture, Foshan University, Foshan, China.
Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Biology, Duke University, Durham, NC 27708, USA. [e-mail] [e-mail] [e-mail].
Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail] [e-mail] [e-mail].
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.03 kDa 
• Atom Count: 1,005 
• Modeled Residue Count: 118 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable disease resistance protein At5g66900	A	135	Arabidopsis thaliana	Mutation(s): 2  Gene Names: At5g66900, MUD21.16
UniProt
Find proteins for Q9FKZ1 (Arabidopsis thaliana) Explore Q9FKZ1  Go to UniProtKB:  Q9FKZ1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.257	α = 90
b = 114.257	β = 90
c = 59.855	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Walton, W.G., Wan, L., Lietzan, A.D., Redinbo, M.R., Dangl, J.L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	IOS-1758400
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	RO1GM107444

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2021-07-14
  Changes: Database references
• Version 1.2: 2021-07-28
  Changes: Database references
• Version 1.3: 2021-09-01
  Changes: Data collection, Database references
• Version 1.4: 2021-09-08
  Changes: Database references
• Version 1.5: 2023-10-18
  Changes: Data collection, Refinement description