[English] 日本語
Yorodumi
- PDB-5oao: Solution structure of the complexed RCD1-RST -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oao
TitleSolution structure of the complexed RCD1-RST
ComponentsRST domain from the Radical-Induced Cell Death1
KeywordsPROTEIN BINDING / alpha-alpha hairpin / hub / L-glove / transcription factor binding
Function / homology
Function and homology information


lateral root morphogenesis / response to ethylene / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to ozone / embryo development ending in seed dormancy / response to water deprivation / programmed cell death / response to superoxide / regulation of reactive oxygen species metabolic process ...lateral root morphogenesis / response to ethylene / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to ozone / embryo development ending in seed dormancy / response to water deprivation / programmed cell death / response to superoxide / regulation of reactive oxygen species metabolic process / response to osmotic stress / NAD+ ADP-ribosyltransferase activity / response to salt stress / nitric oxide biosynthetic process / nuclear matrix / defense response to bacterium / nucleus / cytoplasm
Similarity search - Function
Inactive poly [ADP-ribose] polymerase RCD1/SRO1-5 / RST domain / RCD1-SRO-TAF4 (RST) plant domain / RST domain profile. / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
Inactive poly [ADP-ribose] polymerase RCD1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsBugge, K. / Staby, L. / Skriver, K. / Kragelund, B.B.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish Research Councils4181-00344 Denmark
Novo Nordisk Foundation Denmark
CitationJournal: Structure / Year: 2018
Title: Structure of Radical-Induced Cell Death1 Hub Domain Reveals a Common alpha alpha-Scaffold for Disorder in Transcriptional Networks.
Authors: Bugge, K. / Staby, L. / Kemplen, K.R. / O'Shea, C. / Bendsen, S.K. / Jensen, M.K. / Olsen, J.G. / Skriver, K. / Kragelund, B.B.
History
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RST domain from the Radical-Induced Cell Death1


Theoretical massNumber of molelcules
Total (without water)8,4561
Polymers8,4561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: isothermal titration calorimetry, Kd = 120 nM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6460 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein RST domain from the Radical-Induced Cell Death1 / Protein RADICAL-INDUCED CELL DEATH 1


Mass: 8455.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Complexed with the peptide DREB2A / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RCD1, ATP8, CEO1, At1g32230, F3C3.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RY59

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1133isotropic22D 1H-15N HSQC
1142isotropic32D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCA
151isotropic13D HN(CO)CA
181isotropic13D HNCO
173isotropic23D HNHA
161isotropic13D 1H-15N TOCSY
1101isotropic13D (H)CCH-TOCSY
193isotropic23D 1H-15N NOESY
1123isotropic13D 1H-13C NOESY aliphatic
1113isotropic13D 1H-13C NOESY aromatic
1163isotropic13D 1H-13C NOESY aromatic
1151isotropic13D 1H-15N NOESY
1174isotropic12D 1H-15N IPAP-HSQC
1204anisotropic12D 1H-15N IPAP-HSQC
1193isotropic42D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1200 uM [U-13C; U-15N] RCD1-RST, 200 uM DREB2A, 0.2 mg/mL sodium azide, 0.7 mM DSS, 90% H2O/10% D2O13C15NRST_ulD2A_190% H2O/10% D2O
solution2150 uM [U-15N] RCD1-RST, 150 uM DREB2A, 0.2 mg/mL sodium azide, 0.7 mM DSS, 90% H2O/10% D2O15NRST_ulD2a_190% H2O/10% D2O
solution3200 uM [U-13C; U-15N] RCD1-RST, 200 uM [U-13C; U-15N] DREB2A, 0.2 mg/mL sodium azide, 0.7 mM DSS, 90% H2O/10% D2O2x13C15N90% H2O/10% D2O
solution4300 uM [U-15N] RCD1-RST, 900 uM DREB2A, 50 mg/mL C12E5, 0.2 mg/mL sodium azide, 0.7 mM DSS, 90% H2O/10% D2ORDC90% H2O/10% D2OAnisotropic conditions created by addition of 5% (w/v) pentaethylene monododecyl ether (C12E5)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMRCD1-RST[U-13C; U-15N]1
200 uMDREB2Anatural abundance1
0.2 mg/mLsodium azidenatural abundance1
0.7 mMDSSnatural abundance1
150 uMRCD1-RST[U-15N]2
150 uMDREB2Anatural abundance2
0.2 mg/mLsodium azidenatural abundance2
0.7 mMDSSnatural abundance2
200 uMRCD1-RST[U-13C; U-15N]3
200 uMDREB2A[U-13C; U-15N]3
0.2 mg/mLsodium azidenatural abundance3
0.7 mMDSSnatural abundance3
300 uMRCD1-RST[U-15N]4
900 uMDREB2Anatural abundance4
50 mg/mLC12E5natural abundance4
0.2 mg/mLsodium azidenatural abundance4
0.7 mMDSSnatural abundance4
Sample conditionsIonic strength: 100 mM NaCl mM / Label: Cond1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA8001Room temperature probe
Varian INOVAVarianINOVA7502Room temperature probe
Bruker AVANCEBrukerAVANCE7503Cryo probe
Bruker AVANCEBrukerAVANCE6004Cryo probe

-
Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
PROCHECK / PROCHECK-NMRLaskowski and MacArthurgeometry optimization
VNMRVariancollection
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8 / Details: EEFx
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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