6S2P

Structure of the NB-ARC domain from the Tomato immune receptor NRC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.307 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor.

Steele, J.F.C.Hughes, R.K.Banfield, M.J.

(2019) PLoS One 14: e0221226-e0221226

  • DOI: 10.1371/journal.pone.0221226
  • Primary Citation of Related Structures:  
    6S2P

  • PubMed Abstract: 
  • Plant NLRs are modular immune receptors that trigger rapid cell death in response to attempted infection by pathogens. A highly conserved nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4 (NB-ARC domain) is proposed to act as a molecular switch, cycling between ADP (repressed) and ATP (active) bound forms ...

    Plant NLRs are modular immune receptors that trigger rapid cell death in response to attempted infection by pathogens. A highly conserved nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4 (NB-ARC domain) is proposed to act as a molecular switch, cycling between ADP (repressed) and ATP (active) bound forms. Studies of plant NLR NB-ARC domains have revealed functional similarities to mammalian homologues, and provided insight into potential mechanisms of regulation. However, further advances have been limited by difficulties in obtaining sufficient yields of protein suitable for structural and biochemical techniques. From protein expression screens in Escherichia coli and Sf9 insect cells, we defined suitable conditions to produce the NB-ARC domain from the tomato NLR NRC1. Biophysical analyses of this domain showed it is a folded, soluble protein. Structural studies revealed the NRC1 NB-ARC domain had co-purified with ADP, and confirmed predicted structural similarities between plant NLR NB-ARC domains and their mammalian homologues.


    Related Citations: 
    • Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor
      Steele, J.F.C., Hughes, R.K., Banfield, M.J.
      (2019) Biorxiv --: --

    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, England, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NRC1A [auth N]347Solanum lycopersicumMutation(s): 0 
UniProt
Find proteins for A0A3Q7EK40 (Solanum lycopersicum)
Explore A0A3Q7EK40 
Go to UniProtKB:  A0A3Q7EK40
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
B [auth N]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.307 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.517α = 90
b = 110.517β = 90
c = 53.338γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection
  • Version 1.2: 2019-09-11
    Changes: Data collection, Database references