[English] 日本語
Yorodumi
- EMDB-7290: Drosophila Dicer-2 bound to blunt dsRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7290
TitleDrosophila Dicer-2 bound to blunt dsRNA
Map dataDrosophila Dicer-2 bound to blunt dsRNA substrate
Sample
  • Complex: Drosophila Dicer-2 bound to blunt dsRNA
    • Protein or peptide: Dicer-2, isoform A
    • RNA: RNA (5'-R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*AP*GP*U)-3')
    • RNA: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')
KeywordsDicer / Dcr2 / Dcr-2 / dmDcr-2 / Dicer-2 / helicase / dsRNA / RNA / RNA BINDING PROTEIN / rna binding protein-rna complex
Function / homology
Function and homology information


positive regulation of Toll signaling pathway / : / lncRNA catabolic process / RNAi-mediated antiviral immune response / dsRNA transport / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity ...positive regulation of Toll signaling pathway / : / lncRNA catabolic process / RNAi-mediated antiviral immune response / dsRNA transport / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity / RISC-loading complex / detection of virus / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / 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 / mRNA 3'-UTR binding / locomotory behavior / helicase activity / cellular response to virus / heterochromatin formation / cytoplasmic ribonucleoprotein granule / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / 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 / Ribonuclease III domain ...: / 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 / 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsShen PS / Sinha NK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121706 United States
CitationJournal: Science / Year: 2018
Title: Dicer uses distinct modules for recognizing dsRNA termini.
Authors: Niladri K Sinha / Janet Iwasa / Peter S Shen / Brenda L Bass /
Abstract: Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging ...Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging termini are cleaved distributively. To understand this discrimination, we used cryo-electron microscopy to solve structures of Dicer-2 alone and in complex with blunt dsRNA. Whereas the Platform-PAZ domains have been considered the only Dicer domains that bind dsRNA termini, unexpectedly, we found that the helicase domain is required for binding blunt, but not 3' overhanging, termini. We further showed that blunt dsRNA is locally unwound and threaded through the helicase domain in an adenosine triphosphate-dependent manner. Our studies reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for the discovery of helicase-dependent functions in other Dicers.
History
DepositionDec 9, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseDec 27, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bu9
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7290.png

Downloads & links

-
Map

FileDownload / File: emd_7290.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrosophila Dicer-2 bound to blunt dsRNA substrate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 200 pix.
= 238.6 Å		1.19 Å/pix.
x 200 pix.
= 238.6 Å		1.19 Å/pix.
x 200 pix.
= 238.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.193 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.0105500575 - 0.057273593
Average (Standard dev.)0.00020151319 (±0.0020879514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 238.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1931.1931.193
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z238.600238.600238.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0110.0570.000

-
Supplemental data

-
Sample components

-
Entire : Drosophila Dicer-2 bound to blunt dsRNA

EntireName: Drosophila Dicer-2 bound to blunt dsRNA
Components
  • Complex: Drosophila Dicer-2 bound to blunt dsRNA
    • Protein or peptide: Dicer-2, isoform A
    • RNA: RNA (5'-R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*AP*GP*U)-3')
    • RNA: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')

-
Supramolecule #1: Drosophila Dicer-2 bound to blunt dsRNA

SupramoleculeName: Drosophila Dicer-2 bound to blunt dsRNA / 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: ribonuclease III
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 198.074797 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMEDVEIKP RGYQLRLVDH LTKSNGIVYL PTGSGKTFVA ILVLKRFSQD FDKPIESGGK RALFMCNTVE LARQQAMAVR RCTNFKVGF YVGEQGVDDW TRGMWSDEIK KNQVLVGTAQ VFLDMVTQTY VALSSLSVVI IDECHHGTGH HPFREFMRLF T IANQTKLP ...String:
GPMEDVEIKP RGYQLRLVDH LTKSNGIVYL PTGSGKTFVA ILVLKRFSQD FDKPIESGGK RALFMCNTVE LARQQAMAVR RCTNFKVGF YVGEQGVDDW TRGMWSDEIK KNQVLVGTAQ VFLDMVTQTY VALSSLSVVI IDECHHGTGH HPFREFMRLF T IANQTKLP RVVGLTGVLI KGNEITNVAT KLKELEITYR GNIITVSDTK EMENVMLYAT KPTEVMVSFP HQEQVLTVTR LI SAEIEKF YVSLDLMNIG VQPIRRSKSL QCLRDPSKKS FVKQLFNDFL YQMKEYGIYA ASIAIISLIV EFDIKRRQAE TLS VKLMHR TALTLCEKIR HLLVQKLQDM TYDDDDDNVN TEEVIMNFST PKVQRFLMSL KVSFADKDPK DICCLVFVER RYTC KCIYG LLLNYIQSTP ELRNVLTPQF MVGRNNISPD FESVLERKWQ KSAIQQFRDG NANLMICSSV LEEGIDVQAC NHVFI LDPV KTFNMYVQSK GRARTTEAKF VLFTADKERE KTIQQIYQYR KAHNDIAEYL KDRVLEKTEP ELYEIKGHFQ DDIDPF TNE NGAVLLPNNA LAILHRYCQT IPTDAFGFVI PWFHVLQEDE RDRIFGVSAK GKHVISINMP VNCMLRDTIY SDPMDNV KT AKISAAFKAC KVLYSLGELN ERFVPKTLKE RVASIADVHF EHWNKYGDSV TATVNKADKS KDRTYKTECP LEFYDALP R VGEICYAYEI FLEPQFESCE YTEHMYLNLQ TPRNYAILLR NKLPRLAEMP LFSNQGKLHV RVANAPLEVI IQNSEQLEL LHQFHGMVFR DILKIWHPFF VLDRRSKENS YLVVPLILGA GEQKCFDWEL MTNFRRLPQS HGSNVQQREQ QPAPRPEDFE GKIVTQWYA NYDKPMLVTK VHRELTPLSY MEKNQQDKTY YEFTMSKYGN RIGDVVHKDK FMIEVRDLTE QLTFYVHNRG K FNAKSKAK MKVILIPELC FNFNFPGDLW LKLIFLPSIL NRMYFLLHAE ALRKRFNTYL NLHLLPFNGT DYMPRPLEID YS LKRNVDP LGNVIPTEDI EEPKSLLEPM PTKSIEASVA NLEITEFENP WQKYMEPVDL SRNLLSTYPV ELDYYYHFSV GNV CEMNEM DFEDKEYWAK NQFHMPTGNI YGNRTPAKTN ANVPALMPSK PTVRGKVKPL LILQKTVSKE HITPAEQGEF LAAI TASSA ADVFDMERLE ILGASFLKLS ATLYLASKYS DWNEGTLTEV KSKLVSNRNL LFCLIDADIP KTLNTIQFTP RYTWL PPGI SLPHNVLALW RENPEFAKII GPHNLRDLAL GDEESLVKGN CSDINYNRFV EGCRANGQSF YAGADFSSEV NFCVGL VTI PNKVIADTLE ALLGVIVKNY GLQHAFKMLE YFKICRADID KPLTQLLNLE LGGKKMRANV NTTEIDGFLI NHYYLEK NL GYTFKDRRYL LQALTHPSYP TNRITGSYQE LEFIGAAILD FLISAYIFEN NTKMNPGALT DLRSALVNNT TLACICVR H RLHFFILAEN AKLSEIISKF VNFQESQGHR VTNYVRILLE EADVQPTPLD LDDELDMTEL PHANKCISQE AEKGVPPKG EFNMSTNVDV PKALGDVLEA LIAAVYLDCR DLQRTWEVIF NLFEPELQEF TRKVPINHIR QLVEHKHAKP VFSSPIVEGE TVMVSCQFT CMEKTIKVYG FGSNKDQAKL SAAKHALQQL SKCDA

UniProtKB: Endoribonuclease Dcr-2

-
Macromolecule #2: RNA (5'-R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*...

MacromoleculeName: RNA (5'-R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*AP*GP*U)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 16.781023 KDa
SequenceString:
GGAGGUAGUA GGUUGUAUAG UAGUAAGACC AGACCCUAGA CCAAUUCAUG CC

-
Macromolecule #3: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')

MacromoleculeName: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 16.528768 KDa
SequenceString:
GGCAUGAAUU GGUCUAGGGU CUGGUCUUAC UACUAUACAA CCUACUACCU CC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4a36

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19445
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

+
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