[English] 日本語
Yorodumi
- PDB-7w0d: Dicer2-LoqsPD-dsRNA complex at mid-translocation state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w0d
TitleDicer2-LoqsPD-dsRNA complex at mid-translocation state
Components
  • Dicer-2, isoform A
  • Loquacious, isoform D
  • dsRNA
KeywordsRNA BINDING PROTEIN / Ribonuclease
Function / homology
Function and homology information


positive regulation of Toll signaling pathway / : / lncRNA catabolic process / MicroRNA (miRNA) biogenesis / RNAi-mediated antiviral immune response / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport ...positive regulation of Toll signaling pathway / : / lncRNA catabolic process / MicroRNA (miRNA) biogenesis / RNAi-mediated antiviral immune response / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome / RISC complex binding / global gene silencing by mRNA cleavage / germ-line stem cell population maintenance / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity / RISC-loading complex / miRNA metabolic process / detection of virus / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / pre-miRNA processing / siRNA processing / siRNA binding / positive regulation of innate immune response / ATP-dependent activity, acting on RNA / RISC complex / positive regulation of defense response to virus by host / central nervous system development / mRNA 3'-UTR binding / locomotory behavior / helicase activity / cellular response to virus / heterochromatin formation / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family ...: / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / Endoribonuclease Dcr-2 / Protein Loquacious
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsSu, S. / Wang, J. / Wang, H.W. / Ma, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0503500 China
National Natural Science Foundation of China (NSFC)32000849 China
CitationJournal: Nature / Year: 2022
Title: Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD.
Authors: Shichen Su / Jia Wang / Ting Deng / Xun Yuan / Jinqiu He / Nan Liu / Xiaomin Li / Ying Huang / Hong-Wei Wang / Jinbiao Ma /
Abstract: Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes. In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided ...Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes. In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), has an important role in generating 21 bp siRNA duplexes from long double-stranded RNAs (dsRNAs). ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes. Here we report the cryo-electron microscopy structures of Dcr-2-Loqs-PD in the apo state and in multiple states in which it is processing a 50 bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and substantial conformational changes of Dcr-2 during a dsRNA-processing cycle. The N-terminal helicase and domain of unknown function 283 (DUF283) domains undergo conformational changes after initial dsRNA binding, forming an ATP-binding pocket and a 5'-phosphate-binding pocket. The overall conformation of Dcr-2-Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, whereas the interactions between the DUF283 and RIIIDb domains prevent non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active centre. Additional ATP-dependent conformational changes are required to form an active dicing state and precisely cleave the dsRNA into a 21 bp siRNA duplex as confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full cycle of ATP-dependent dsRNA processing by Dcr-2-Loqs-PD.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.year / _struct.title
Revision 1.2Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Loquacious, isoform D
D: dsRNA
G: Loquacious, isoform D
A: Dicer-2, isoform A
F: Dicer-2, isoform A
C: dsRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,21510
Polymers506,3126
Non-polymers9034
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Loquacious, isoform D


Mass: 38502.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: loqs, cg6866, Dmel\CG6866, dRax, loq, LOQS, Loqs, Loqs-PD, LqPD, R3D1, r3d1, R3D1-L, R3D1-S, TRBP, CG6866, Dmel_CG6866
Production host: Escherichia coli (E. coli) / References: UniProt: M9MRT5
#2: RNA chain dsRNA


Mass: 16646.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Protein Dicer-2, isoform A / FI15132p1


Mass: 198006.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Dcr-2, cg6493, Dcr, dcr, DCR-2, dcr-2, Dcr-2-RA, DCR2, Dcr2, dcr2, dDcr2, dic2, DICER, Dicer, dicer, DICER-2, dicer-2, Dicer2, dicer2, dmDcr-2, Dmel\CG6493, CG6493, Dmel_CG6493
Production host: Escherichia coli (E. coli)
References: UniProt: A1ZAW0, deoxyribonuclease I, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters, ribonuclease III, adenosinetriphosphatase
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Dicer2-LoqsPD-dsRNA complex at its mid-translocation state
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71991 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00220952
ELECTRON MICROSCOPYf_angle_d0.56428839
ELECTRON MICROSCOPYf_dihedral_angle_d7.0733691
ELECTRON MICROSCOPYf_chiral_restr0.0393334
ELECTRON MICROSCOPYf_plane_restr0.0043299

+
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