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- PDB-6bu9: Drosophila Dicer-2 bound to blunt dsRNA -

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Entry
Database: PDB / ID: 6bu9
TitleDrosophila Dicer-2 bound to blunt dsRNA
DescriptorDicer-2, isoform A/RNA Complex
Keywordsrna binding protein/rna / Dicer / Dcr2 / Dcr-2 / dmDcr-2 / Dicer-2 / helicase / dsRNA / RNA / RNA BINDING PROTEIN / rna binding protein-rna complex
Specimen sourceDrosophila melanogaster / arthropod / Fruit fly / キイロショウジョウバエ /
Unidentified
MethodElectron microscopy (6.8 Å resolution / Particle / Single particle)
AuthorsShen, P.S. / Sinha, N.K. / Bass, B.L.
CitationScience, 2017

Science, 2017 Yorodumi Papers
Dicer uses distinct modules for recognizing dsRNA termini.
Niladri K Sinha / Janet Iwasa / Peter S Shen / Brenda L Bass

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 9, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Jan 3, 2018Structure modelDatabase referencescitation_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
1.2Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Dicer-2, isoform A
B: 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')
C: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)231,3853
Polyers231,3853
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Dicer-2, isoform A / FI15132p1


Mass: 198074.797 Da / Num. of mol.: 1
Source: (gene. exp.) Drosophila melanogaster / arthropod / キイロショウジョウバエ /
References: UniProt: A1ZAW0, EC: 3.1.26.3, EC: 3.6.1.3
#2: RNA chainRNA (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')


Mass: 16781.023 Da / Num. of mol.: 1 / Source: (synth.) Unidentified
#3: RNA chainRNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')


Mass: 16528.768 Da / Num. of mol.: 1 / Source: (synth.) Unidentified

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Drosophila Dicer-2 bound to blunt dsRNA / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster
Source (recombinant)Organism: Spodoptera frugiperda
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 19445 / Symmetry type: POINT

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