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- EMDB-15298: Mouse endoribonuclease Dicer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15298
TitleMouse endoribonuclease Dicer
Map dataLocally refined map of Dicer core region.
Sample
  • Organelle or cellular component: Free form of mouse somatic dicer
Keywordsendoribonuclease / gene silencing / post-transcriptional / catalytic enzyme / cytoplasm / RNA BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsZanova M / Zapletal D / Kubicek K / Stefl R / Pinkas M / Novacek J
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
Czech Science FoundationGA22-19896S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: To Be Published
Title: Mammalian Dicer uses its helicase domain to control RNA processing
Authors: Zapletal D / Kubicek K / Zanova M / Sebesta M / Pinkas M / Malik R / Joseph DF / Novacek J / Svoboda P / Stefl R
History
DepositionJul 1, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15298.png

Downloads & links

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Map

FileDownload / File: emd_15298.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally refined map of Dicer core region.
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.0463
Minimum - Maximum-0.3383622 - 2.2260807
Average (Standard dev.)0.0005049407 (±0.016722217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_15298_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_15298_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Free form of mouse somatic dicer

EntireName: Free form of mouse somatic dicer
Components
  • Organelle or cellular component: Free form of mouse somatic dicer

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Supramolecule #1: Free form of mouse somatic dicer

SupramoleculeName: Free form of mouse somatic dicer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.20 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMTris
100.0 mMSodium Chloride
1.0 mMDithiotreitol
2.0 mMMagensium Chloride

Details: The buffer was always prepared fresh
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Described in STAR methods.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6354 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 862842
Startup modelType of model: NONE
Final reconstructionNumber classes used: 81 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1)
Details: Masked and locally refined electron density map of Dicer core region
Number images used: 92906
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 100 / Avg.num./class: 1377 / Software - Name: cryoSPARC (ver. v3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsEndoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting into combined map from locally refined protein parts was done using Chimera and then Coot's Real Space Refine Zone.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8
Target criteria: Ramachandran Plot, Rotamer Analysis, Density Analysis

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Atomic model buiding 2

DetailsPHENIX Real-space refinement was used for flexible fitting.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 / Target criteria: Correlation coefficient

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Atomic model buiding 3

DetailsISOLDE was used for flexible fitting with defined torsion restraints
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8
Target criteria: Ramachandran Plot, Rotamer Analysis, Clash Score

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