[English] 日本語
Yorodumi
- PDB-6i3r: Structure, dynamics and roX2-lncRNA binding of tandem double-stra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i3r
TitleStructure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1/2 of Drosophila helicase MLE
ComponentsDosage compensation regulator
KeywordsRNA BINDING PROTEIN / Helicase / dsRBD
Function / homology
Function and homology information


RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / dosage compensation complex assembly / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulatory region RNA binding / regulation of cytoplasmic translation / PKR-mediated signaling / MSL complex ...RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / dosage compensation complex assembly / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulatory region RNA binding / regulation of cytoplasmic translation / PKR-mediated signaling / MSL complex / dosage compensation by hyperactivation of X chromosome / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / sex-chromosome dosage compensation / 3'-5' RNA helicase activity / regulation of mRNA processing / axon extension / lncRNA binding / DNA duplex unwinding / 3'-5' DNA helicase activity / nuclear chromosome / positive regulation of heterochromatin formation / X chromosome / DNA helicase activity / determination of adult lifespan / helicase activity / double-stranded RNA binding / chromosome / double-stranded DNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / chromatin binding / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dosage compensation regulator mle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsJagtap, P.K.A. / Buelow, S.v. / Masiewicz, P. / Simon, B. / Hennig, J.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless.
Authors: Ankush Jagtap, P.K. / Muller, M. / Masiewicz, P. / von Bulow, S. / Hollmann, N.M. / Chen, P.C. / Simon, B. / Thomae, A.W. / Becker, P.B. / Hennig, J.
History
DepositionNov 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_related
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Revision 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dosage compensation regulator


Theoretical massNumber of molelcules
Total (without water)28,5901
Polymers28,5901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21270 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Dosage compensation regulator / ATP-dependent RNA helicase mle / Protein male-less / Protein maleless / Protein no action potential


Mass: 28589.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mle, nap, CG11680 / Production host: Escherichia coli (E. coli) / References: UniProt: P24785, RNA helicase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic33D (H)CCH-TOCSY
131isotropic33D HN(CA)CB
141isotropic33D HNCA
151isotropic33D CBCA(CO)NH
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D H(CCO)NH
181isotropic13D HNCO
191isotropic13D HBHA(CO)NH
1101isotropic13D 1H-15N NOESY
1111isotropic32D 1H-13C HSQC aromatic
1121isotropic13D 1H-13C NOESY aromatic

-
Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] MLE dsRBD1,2, 90% H2O/10% D2O
Label: 13C, 15N labelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: MLE dsRBD1,2 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 20mM NaPi ph 6.5, 200mM NaCl, 1mM DTT / Ionic strength: 200 mM / Label: NMR Buffer / pH: 6 / Pressure: 1 bar / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8003

-
Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / 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