[English] 日本語
Yorodumi
- PDB-8kfp: Solution structure of Drosophila melanogaster R2D2 dsRBD1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8kfp
TitleSolution structure of Drosophila melanogaster R2D2 dsRBD1
ComponentsR2D2
KeywordsRNA BINDING PROTEIN / RNAi / siRNA / Dicer-2 / dsRNA
Function / homology
Function and homology information


follicle cell of egg chamber stalk formation / regulation of regulatory ncRNA processing / RISC-loading complex / RISC complex assembly / siRNA processing / siRNA binding / RISC complex / double-stranded RNA binding / defense response to virus / nucleus / cytoplasm
Similarity search - Function
: / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / molecular dynamics
Model detailsMODEL GENERATED BY ROSETTA VERSION 2021.16+release.8ee4f02
AuthorsAute, R. / Deshmukh, M.V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP161 India
CitationJournal: Biophys.Chem. / Year: 2024
Title: Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway.
Authors: Aute, R. / Waghela, N. / Deshmukh, M.V.
History
DepositionAug 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: R2D2


Theoretical massNumber of molelcules
Total (without water)11,3121
Polymers11,3121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable, gel filtration, Elutes as a monomer as evaluated by SEC, isothermal titration calorimetry, binds to canonical dsRNA substrates, NMR relaxation ...Evidence: NMR Distance Restraints, not applicable, gel filtration, Elutes as a monomer as evaluated by SEC, isothermal titration calorimetry, binds to canonical dsRNA substrates, NMR relaxation study, Rotational correlation time and the order parameter suggest that R2D2 dsRBD1 is a globular protein corresponding to a monomeric state.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein R2D2


Mass: 11311.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: dsRBD1 of R2D2 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: r2d2 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2Q0L0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D HNCO
152isotropic13D HN(CA)CB
162isotropic13D HN(CA)CO
172isotropic13D HN(COCA)CB
182isotropic13D H(CCO)NH TOCSY
192isotropic13D C(CO)NH TOCSY
1102isotropic13D 1H-15N NOESY
1112isotropic13D 1H-13C NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM [U-99% 15N] R2D2 dsRBD1, 90% H2O/10% D2O50 mM Kphosphate (pH 7.0), 50 mM Na2SO4, 50 mM NaCl, and 2 mM DTT15N90% H2O/10% D2O
solution2500 uM [U-99% 13C; U-99% 15N] R2D2 dsRBD1, 90% H2O/10% D2O50 mM Kphosphate (pH 7.0), 50 mM Na2SO4, 50 mM NaCl, and 2 mM DTT13C, 15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMR2D2 dsRBD1[U-99% 15N]1
500 uMR2D2 dsRBD1[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 150 mM / Label: conditions _1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichchemical shift assignment
Rosetta2021.16.61629Raman, S., Lange, O. F., Rossi, P., Tyka, M., Wang, X., Aramini, J., ... & Baker, D. (2010). NMR structure determination for larger proteins using backbone-only data. Science, 327(5968), 1014-1018.structure calculation
CARA1.8.4Keller and Wuthrichpeak picking
TopSpin2.1Bruker Biospincollection
TopSpin4.0.6Bruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / 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