[English] 日本語
Yorodumi
- PDB-7xoz: Crystal structure of RPPT-TIR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xoz
TitleCrystal structure of RPPT-TIR
Components(ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase) x 2
KeywordsHYDROLASE / NLR / Plant Protein / Plant immune signaling
Function / homology
Function and homology information


ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / defense response / ADP binding / signal transduction / ATP binding
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Leucine Rich Repeat ...Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Leucine Rich Repeat / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsSong, W. / Jia, A. / Huang, S. / Chai, J.
Funding support Germany, China, 2items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2022
Title: TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity.
Authors: Aolin Jia / Shijia Huang / Wen Song / Junli Wang / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Jiao Hou / Tiantian Zhang / Wenquan Yu / Giuliana Hessler / ...Authors: Aolin Jia / Shijia Huang / Wen Song / Junli Wang / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Jiao Hou / Tiantian Zhang / Wenquan Yu / Giuliana Hessler / Ertong Li / Shoucai Ma / Dongli Yu / Jan Gebauer / Ulrich Baumann / Xiaohui Liu / Zhifu Han / Junbiao Chang / Jane E Parker / Jijie Chai /
Abstract: Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain converges on Enhanced Disease ...Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain converges on Enhanced Disease Susceptibility 1 (EDS1) and its direct partners, Phytoalexin Deficient 4 (PAD4) or Senescence-Associated Gene 101 (SAG101). TIR-encoded nicotinamide adenine dinucleotide hydrolase (NADase) produces signaling molecules to promote exclusive EDS1-PAD4 and EDS1-SAG101 interactions with helper NLR subclasses. In this work, we show that TIR-containing proteins catalyze adenosine diphosphate (ADP)-ribosylation of adenosine triphosphate (ATP) and ADP ribose (ADPR) through ADPR polymerase-like and NADase activity, forming ADP-ribosylated ATP (ADPr-ATP) and ADPr-ADPR (di-ADPR), respectively. Specific binding of ADPr-ATP or di-ADPR allosterically promotes EDS1-SAG101 interaction with helper NLR N requirement gene 1A (NRG1A) in vitro and in planta. Our data reveal an enzymatic activity of TIRs that enables specific activation of the EDS1-SAG101-NRG1 immunity branch.
History
DepositionMay 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
B: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
E: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
F: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8866
Polymers75,7674
Non-polymers1,1192
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.799, 81.133, 70.713
Angle α, β, γ (deg.)90.00, 112.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase


Mass: 18936.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AN1_LOCUS14779 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A654FE24, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase


Mass: 18946.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AN1_LOCUS14764 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A654FCP3
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 20 % w/v polyethylene glycol 3000 (PEG3000), 100 mM HEPES pH 7.5, 200 mM sodium

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.52→39.12 Å / Num. obs: 24611 / % possible obs: 98.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 49.84 Å2 / Rpim(I) all: 0.142 / Rrim(I) all: 0.293 / Net I/σ(I): 4
Reflection shellResolution: 2.52→2.61 Å / Num. unique obs: 2370 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
PHENIX1.20_4478refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CRC

7crc


Resolution: 2.52→39.12 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 1225 5.02 %
Rwork0.2575 --
obs0.2595 24380 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 72 42 5266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.92
X-RAY DIFFRACTIONf_dihedral_angle_d13.422036
X-RAY DIFFRACTIONf_chiral_restr0.053804
X-RAY DIFFRACTIONf_plane_restr0.007884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.620.40921290.38842380X-RAY DIFFRACTION92
2.62-2.740.42881360.3592541X-RAY DIFFRACTION99
2.74-2.890.39561370.35322588X-RAY DIFFRACTION99
2.89-3.070.36821370.32862611X-RAY DIFFRACTION100
3.07-3.30.32621360.26812575X-RAY DIFFRACTION100
3.3-3.640.30411420.25252605X-RAY DIFFRACTION100
3.64-4.160.23531350.21372610X-RAY DIFFRACTION99
4.16-5.240.23911320.2022600X-RAY DIFFRACTION100
5.24-39.120.28031410.2432645X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2203-0.48480.13732.1229-0.22873.28570.13880.1541-0.2217-0.15270.0120.15470.0404-0.1790.01890.3083-0.0703-0.01240.21980.07490.3244-25.7461.17339.448
22.91280.75550.25691.8212-0.25421.63720.0861-0.4045-0.01990.0325-0.0946-0.16790.16740.3676-0.00010.5102-0.0628-0.04750.85340.09480.5675-34.9791.217.087
32.8529-0.5966-0.10943.1027-0.59083.59580.1574-0.5738-0.05080.14020.1693-0.1406-0.00190.15070.74510.2565-0.081-0.00730.16390.09430.16410.2280.9946.111
42.420.04180.82633.258-0.07732.17030.2623-0.0735-0.32870.2582-0.1031-0.00820.07340.3110.01510.4364-0.075-0.0490.60960.08790.4228.3751.2440.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:166 )A2 - 166
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:166 )B2 - 166
3X-RAY DIFFRACTION3( CHAIN E AND RESID 4:166 )E4 - 166
4X-RAY DIFFRACTION4( CHAIN F AND RESID 4:166 )F4 - 166

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more