7S2Z | pdb_00007s2z

Crystal structure of the E100A mutant TIR domain from the grapevine disease resistance protein RUN1 bound to NAD

PDB DOI: https://doi.org/10.2210/pdb7S2Z/pdb

Classification: SIGNALING PROTEIN,HYDROLASE
Organism(s): Vitis rotundifolia
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2021-09-04 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: 2.35 Å
R-Value Free:
0.255 (Depositor), 0.256 (DCC)
R-Value Work:
0.218 (Depositor), 0.219 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 87 kDa
Atom Count: 5,988
Modeled Residue Count: 684
Deposited Residue Count: 716
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease resistance protein RUN1	A, B, C, D	179	Vitis rotundifolia	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V9M398
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	E [auth A], K [auth B], Q [auth C], V [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255 (Depositor), 0.256 (DCC)
R-Value Work: 0.218 (Depositor), 0.219 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.743	α = 90
b = 116.644	β = 90
c = 122.22	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-13

Deposition Author(s):

Burdett, H.

Kobe, B.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP160102244
Australian Research Council (ARC)	Australia	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
Version 1.2: 2024-11-13
Changes: Structure summary