7RTS

Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1 without the AE interface

PDB DOI: https://doi.org/10.2210/pdb7RTS/pdb

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

Deposited: 2021-08-15 Released: 2021-10-13
Deposition Author(s): Burdett, H., Kobe, B.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.229
R-Value Work: 0.198
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 21.1 kDa
Atom Count: 1,421
Modelled Residue Count: 163
Deposited Residue Count: 179
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease resistance protein RUN1	A	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V9M398
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.229
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.37	α = 90
b = 50.37	β = 90
c = 120.313	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-13

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2021-10-13
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.