[English] 日本語
Yorodumi
- PDB-8z49: Solution Structure of DRB7.2 M, the dsRBD region of DRB7.2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z49
TitleSolution Structure of DRB7.2 M, the dsRBD region of DRB7.2
ComponentsDouble-stranded RNA-binding domain (DsRBD)-containing protein
KeywordsPLANT PROTEIN / RNAi / DRB4 / Gene regulation / endo-IR pathway
Function / homologydouble strand RNA binding domain from DEAD END PROTEIN 1 / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / RNA binding / Double-stranded RNA-binding domain (DsRBD)-containing protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDeshmukh, M.V. / Paturi, S. / Patra, D.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP0161 India
CitationJournal: Elife / Year: 2025
Title: The mechanism of DRB7.2:DRB4 mediated sequestering of endogenous inverted-repeat dsRNA precursors in plants
Authors: Paturi, S. / Patra, D. / Behera, P.C. / Aute, R. / Waghela, N. / Kinatukara, P. / Deshmukh, M.V.
History
DepositionApr 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Double-stranded RNA-binding domain (DsRBD)-containing protein


Theoretical massNumber of molelcules
Total (without water)11,0031
Polymers11,0031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, not applicable, NMR relaxation study, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Double-stranded RNA-binding domain (DsRBD)-containing protein


Mass: 11002.543 Da / Num. of mol.: 1 / Fragment: Double-stranded RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4G00420 / Plasmid: pETtrx-1b / Details (production host): N-terminal TRX tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: F4JHB3
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D HN(COCA)CB
151isotropic13D HN(CA)CB
1181isotropic13D HNCA
1171isotropic13D HN(CO)CA
2162isotropic13D (H)C(CCO)NH TOCSY
2152isotropic13D H(CCO)NH TOCSY
1141anisotropic12D 1H-15N IPAP HSQC
2132isotropic13D 1H-13C NOESY
2122isotropic13D 1H-15N NOESY
1111isotropic13D 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1400 uM U-[15N,13C],2H-[~90%] DRB7.2 dsRBD, 90% H2O/10% D2OU[15N,13C],2H[~90%] DRB7.2M complexed with U-[2H] DRB4D3U-[15N,13C],2H-[~90%]90% H2O/10% D2O
solution2400 uM U-[15N,13C],2H-[~50%] DRB7.2 dsRBD, 90% H2O/10% D2OU[15N,13C],2H[~50%] DRB7.2M complexed with U-[2H] DRB4D3U-[15N,13C],2H-[~50%]90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMDRB7.2 dsRBDU-[15N,13C],2H-[~90%]1
400 uMDRB7.2 dsRBDU-[15N,13C],2H-[~50%]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1U[15N,13C],2H[~90%] DRB7.2M : U-[2H] DRB4D3150 mM171 bar298 K
2U[15N,13C],2H[~50%] DRB7.2M : U-[2H] DRB4D3150 mM271 bar298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RosettaDavid Bakerrefinement
CARAKeller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10

+
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