7RX1 | pdb_00007rx1

Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1

• PDB DOI: https://doi.org/10.2210/pdb7RX1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vitis rotundifolia
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-08-21 Released: 2021-10-13 
• Deposition Author(s): Burdett, H., Kobe, B.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Self-association configures the NAD + -binding site of plant NLR TIR domains

Burdett, H., Hu, X., Rank, M.X., Maruta, N., Kobe, B.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.10.02.462850

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.1 kDa 
• Atom Count: 2,980 
• Modeled Residue Count: 345 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease resistance protein RUN1	A, B	179	Vitis rotundifolia	Mutation(s): 0  Gene Names: RUN1 EC: 3.2.2.6 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt
Find proteins for V9M398 (Vitis rotundifolia) Explore V9M398  Go to UniProtKB:  V9M398

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.435	α = 90
b = 41.471	β = 118.514
c = 77.232	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Burdett, H., Kobe, B.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP160102244
Australian Research Council (ARC)	Australia	DP190102526

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary