[English] 日本語
Yorodumi
- PDB-7rx1: Crystal structure of the TIR domain from the grapevine disease re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rx1
TitleCrystal structure of the TIR domain from the grapevine disease resistance protein RUN1
ComponentsDisease resistance protein RUN1
KeywordsSIGNALING PROTEIN / NAD+ Hydrolase / Signalling Protein / TIR domain / NAD+ nucleosidase activity
Function / homology
Function and homology information


NADP+ nucleosidase activity / NAD+ catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction ...NADP+ nucleosidase activity / NAD+ catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction / nucleus / cytoplasm
Similarity search - Function
C-JID domain / C-JID domain / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / TIR domain ...C-JID domain / C-JID domain / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / TIR domain / 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, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disease resistance protein RUN1
Similarity search - Component
Biological speciesVitis rotundifolia (muscadine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsBurdett, H. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
CitationJournal: Biorxiv / Year: 2021
Title: Self-association configures the NAD + -binding site of plant NLR TIR domains
Authors: Burdett, H. / Hu, X. / Rank, M.X. / Maruta, N. / Kobe, B.
History
DepositionAug 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disease resistance protein RUN1
B: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0999
Polymers41,4272
Non-polymers6727
Water2,072115
1
A: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0024
Polymers20,7131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0985
Polymers20,7131
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.435, 41.471, 77.232
Angle α, β, γ (deg.)90.000, 118.514, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Disease resistance protein RUN1 / NAD(+) hydrolase RUN1 / NADP(+) hydrolase RUN1 / Resistance to Uncinula necator protein / MrRUN1


Mass: 20713.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis rotundifolia (muscadine) / Gene: RUN1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: V9M398, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Lithium Sulfate, 0.1 M HEPES pH 7, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→33.93 Å / Num. obs: 34128 / % possible obs: 99.48 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.67 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Net I/σ(I): 12.06
Reflection shellResolution: 1.892→1.959 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.262 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3294 / CC1/2: 0.358 / CC star: 0.726 / Rpim(I) all: 0.801 / Rrim(I) all: 0.074 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o0w

6o0w


Resolution: 1.89→33.93 Å / SU ML: 0.2515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 1627 4.77 %
Rwork0.2008 32491 -
obs0.202 34118 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 1.89→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 35 115 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792924
X-RAY DIFFRACTIONf_angle_d0.80723938
X-RAY DIFFRACTIONf_chiral_restr0.0521402
X-RAY DIFFRACTIONf_plane_restr0.0077508
X-RAY DIFFRACTIONf_dihedral_angle_d28.9654390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.950.35371230.31912600X-RAY DIFFRACTION97.11
1.95-2.010.33031320.29322694X-RAY DIFFRACTION99.86
2.01-2.080.28571400.27392718X-RAY DIFFRACTION99.9
2.08-2.170.33131210.2632663X-RAY DIFFRACTION99.82
2.17-2.260.28751300.23742720X-RAY DIFFRACTION99.75
2.26-2.380.28611360.22982708X-RAY DIFFRACTION99.82
2.38-2.530.29331560.2242682X-RAY DIFFRACTION99.89
2.53-2.730.24411330.22592716X-RAY DIFFRACTION99.79
2.73-30.26381420.23212707X-RAY DIFFRACTION99.75
3-3.440.22691290.21652734X-RAY DIFFRACTION99.62
3.44-4.330.18731330.16862749X-RAY DIFFRACTION99.59
4.33-33.930.16261520.14682800X-RAY DIFFRACTION99.19

+
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