3JRN | pdb_00003jrn

Crystal structure of TIR domain from Arabidopsis Thaliana

• PDB DOI: https://doi.org/10.2210/pdb3JRN/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-08 Released: 2009-10-20 
• Deposition Author(s): Chan, S.L., Mukasa, T., Santelli, E., Low, L.Y., Pascual, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.182 (DCC) 

Literature

The crystal structure of a TIR domain from Arabidopsis thaliana reveals a conserved helical region unique to plants.

Chan, S.L., Mukasa, T., Santelli, E., Low, L.Y., Pascual, J.

(2009) Protein Sci 19: 155-161

• PubMed: 19845004 
• DOI: https://doi.org/10.1002/pro.275
• Primary Citation Related Structures: 
  3JRN


• PubMed Abstract: 
  

  Plants use a highly evolved immune system to exhibit defense response against microbial infections. The plant TIR domain, together with the nucleotide-binding (NB) domain and/or a LRR region, forms a type of molecule, named resistance (R) proteins, that interact with microbial effector proteins and elicit hypersensitive responses against infection. Here, we report the first crystal structure of a plant TIR domain from Arabidopsis thaliana (AtTIR) solved at a resolution of 2.0 A. The structure consists of five beta-strands forming a parallel beta-sheet at the core of the protein. The beta-strands are connected by a series of alpha-helices and the overall fold mimics closely that of other mammalian and bacterial TIR domains. However, the region of the alphaD-helix reveals significant differences when compared with other TIR structures, especially the alphaD3-helix that corresponds to an insertion only present in plant TIR domains. Available mutagenesis data suggest that several conserved and exposed residues in this region are involved in the plant TIR signaling function.

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Organizational Affiliation: 
• Infectious Diseases Center, Burnham Institute for Medical Research, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.35 kDa 
• Atom Count: 1,357 
• Modeled Residue Count: 151 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT1G72930 protein	A	176	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AT1G72930, At1g72930/F3N23.13, AtTIR, F3N23.13
UniProt
Find proteins for Q9SSN3 (Arabidopsis thaliana) Explore Q9SSN3  Go to UniProtKB:  Q9SSN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARS	B [auth A]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.182 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.21	α = 90
b = 71.21	β = 90
c = 60.27	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Chan, S.L., Mukasa, T., Santelli, E., Low, L.Y., Pascual, J.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations