[English] 日本語
Yorodumi
- EMDB-32241: dmDicer2-LoqsPD-dsRNA Post-dicing status -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32241
TitledmDicer2-LoqsPD-dsRNA Post-dicing status
Map data
Sample
  • Complex: Dicer2-LoqsPD-dsRNA complex at its post-dicing state
    • Protein or peptide: Dicer-2, isoform A
    • Protein or peptide: Loquacious, isoform D
    • RNA: siRNA
KeywordsRibonuclease / RNA BINDING PROTEIN
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
Endoribonuclease Dcr-2 / Protein Loquacious
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.55 Å
AuthorsSu S / Wang J / Wang HW / Ma J
Funding support China, 2 items
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, 2021-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32241.png

Downloads & links

-
Map

FileDownload / File: emd_32241.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 259.2 Å		1.08 Å/pix.
x 240 pix.
= 259.2 Å		1.08 Å/pix.
x 240 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.26906583 - 0.8159921
Average (Standard dev.)0.0010577403 (±0.034126136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Dicer2-LoqsPD-dsRNA complex at its post-dicing state

EntireName: Dicer2-LoqsPD-dsRNA complex at its post-dicing state
Components
  • Complex: Dicer2-LoqsPD-dsRNA complex at its post-dicing state
    • Protein or peptide: Dicer-2, isoform A
    • Protein or peptide: Loquacious, isoform D
    • RNA: siRNA

-
Supramolecule #1: Dicer2-LoqsPD-dsRNA complex at its post-dicing state

SupramoleculeName: Dicer2-LoqsPD-dsRNA complex at its post-dicing state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
Macromolecule #1: Dicer-2, isoform A

MacromoleculeName: Dicer-2, isoform A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 198.008656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEDVEIKPRG YQLRLVDHLT KSNGIVYLPT GSGKTFVAIL VLKRFSQDFD KPIESGGKRA LFMCNTVELA RQQAMAVRRC TNFKVGFYV GEQGVDDWTR GMWSDEIKKN QVLVGTAQVF LDMVTQTYVA LSSLSVVIID ECHHGTGHHP FREFMRLFTI A NQTKLPRV ...String:
MEDVEIKPRG YQLRLVDHLT KSNGIVYLPT GSGKTFVAIL VLKRFSQDFD KPIESGGKRA LFMCNTVELA RQQAMAVRRC TNFKVGFYV GEQGVDDWTR GMWSDEIKKN QVLVGTAQVF LDMVTQTYVA LSSLSVVIID ECHHGTGHHP FREFMRLFTI A NQTKLPRV VGLTGVLIKG NEITNVATKL KELEITYRGN IITVSDTKEM ENVMLYATKP TEVMVSFPHQ EQVLTVTRLI SA EIEKFYV SLDLMNIGVQ PIRRSKSLQC LRDPSKKSFV KQLFNDFLYQ MKEYGIYAAS IAIISLIVEF DIKRRQAETL SVK LMHRTA LTLCEKIRHL LVQKLQDMTY DDDDDNVNTE EVIMNFSTPK VQRFLMSLKV SFADKDPKDI CCLVFVERRY TCKC IYGLL LNYIQSTPEL RNVLTPQFMV GRNNISPDFE SVLERKWQKS AIQQFRDGNA NLMICSSVLE EGIDVQACNH VFILD PVKT FNMYVQSKGR ARTTEAKFVL FTADKEREKT IQQIYQYRKA HNDIAEYLKD RVLEKTEPEL YEIKGHFQDD IDPFTN ENG AVLLPNNALA ILHRYCQTIP TDAFGFVIPW FHVLQEDERD RIFGVSAKGK HVISINMPVN CMLRDTIYSD PMDNVKT AK ISAAFKACKV LYSLGELNER FVPKTLKERV ASIADVHFEH WNKYGDSVTA TVNKADKSKD RTYKTECPLE FYDALPRV G EICYAYEIFL EPQFESCEYT EHMYLNLQTP RNYAILLRNK LPRLAEMPLF SNQGKLHVRV ANAPLEVIIQ NSEQLELLH QFHGMVFRDI LKIWHPFFVL DRRSKENSYL VVPLILGAGE QKCFDWELMT NFRRLPQSHG SNVQQREQQP APRPEDFEGK IVTQWYANY DKPMLVTKVH RELTPLSYME KNQQDKTYYE FTMSKYGNRI GDVVHKDKFM IEVRDLTEQL TFYVHNRGKF N AKSKAKMK VILIPELCFN FNFPGDLWLK LIFLPSILNR MYFLLHAEAL RKRFNTYLNL HLLPFNGTDY MPRPLEIDYS LK RNVDPLG NVIPTEDIEE PKSLLEPMPT KSIEASVANL EITEFENPWQ KYMEPVDLSR NLLSTYPVEL DYYYHFSVGN VCE MNEMDF EDKEYWAKNQ FHMPTGNIYG NRTPAKTNAN VPALMPSKPT VRGKVKPLLI LQKTVSKEHI TPAEQGEFLA AITA SSAAD VFDMERLEIL GDSFLKLSAT LYLASKYSDW NEGTLTEVKS KLVSNRNLLF CLIDADIPKT LNTIQFTPRY TWLPP GISL PHNVLALWRE NPEFAKIIGP HNLRDLALGD EESLVKGNCS DINYNRFVEG CRANGQSFYA GADFSSEVNF CVGLVT IPN KVIADTLEAL LGVIVKNYGL QHAFKMLEYF KICRADIDKP LTQLLNLELG GKKMRANVNT TEIDGFLINH YYLEKNL GY TFKDRRYLLQ ALTHPSYPTN RITGSYQELE FIGDAILDFL ISAYIFENNT KMNPGALTDL RSALVNNTTL ACICVRHR L HFFILAENAK LSEIISKFVN FQESQGHRVT NYVRILLEEA DVQPTPLDLD DELDMTELPH ANKCISQEAE KGVPPKGEF NMSTNVDVPK ALGDVLEALI AAVYLDCRDL QRTWEVIFNL FEPELQEFTR KVPINHIRQL VEHKHAKPVF SSPIVEGETV MVSCQFTCM EKTIKVYGFG SNKDQAKLSA AKHALQQLSK CDA

UniProtKB: Endoribonuclease Dcr-2

-
Macromolecule #2: Loquacious, isoform D

MacromoleculeName: Loquacious, isoform D / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 38.502574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDQENFHGSS LPQQLQNLHI QPQQASPNPV QTGFAPRRHY NNLVGLGNGN AVSGSPVKGA PLGQRHVKLK KEKISAQVAQ LSQPGQLQL SDVGDPALAG GSGLQGGVGL MGVILPSDEA LKFVSETDAN GLAMKTPVSI LQELLSRRGI TPGYELVQIE G AIHEPTFR ...String:
MDQENFHGSS LPQQLQNLHI QPQQASPNPV QTGFAPRRHY NNLVGLGNGN AVSGSPVKGA PLGQRHVKLK KEKISAQVAQ LSQPGQLQL SDVGDPALAG GSGLQGGVGL MGVILPSDEA LKFVSETDAN GLAMKTPVSI LQELLSRRGI TPGYELVQIE G AIHEPTFR FRVSFKDKDT PFTAMGAGRS KKEAKHAAAR ALIDKLIGAQ LPESPSSSAG PSVTGLTVAG SGGDGNANAT GG GDASDKT VGNPIGWLQE MCMQRRWPPP SYETETEVGL PHERLFTIAC SILNYREMGK GKSKKIAKRL AAHRMWMRLQ ETP IDSGKI SDSICGELEG EVSIIQDIDR YEQVSKDFEF IKI

UniProtKB: Protein Loquacious

-
Macromolecule #3: siRNA

MacromoleculeName: siRNA / type: rna / ID: 3 / Number of copies: 4
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 16.646871 KDa
SequenceString:
GAGACUUGGG CAAUGUGACU GCUGAUCAGC AGUCACAUUG CCCAAGUCUC UU

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 82469
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7w0f:
dmDicer2-LoqsPD-dsRNA Post-dicing status

+
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