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- EMDB-7290: Drosophila Dicer-2 bound to blunt dsRNA -

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Basic information

Entry
Database: EMDB / ID: 7290
TitleDrosophila Dicer-2 bound to blunt dsRNA
SampleDrosophila Dicer-2 bound to blunt dsRNA
SourceDrosophila melanogaster / arthropod / キイロショウジョウバエ /
Map dataDrosophila Dicer-2 bound to blunt dsRNA substrate
Methodsingle particle reconstruction, at 6.8 Å resolution
AuthorsShen PS / Sinha NK
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 ReportPDB-ID: 6bu9

SummaryFull reportAbout validation report
DateDeposition: Dec 9, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Jan 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6bu9
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_7290.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.19 Å/pix.
= 238.6 Å
200 pix
1.19 Å/pix.
= 238.6 Å
200 pix
1.19 Å/pix.
= 238.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.193 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.0105500575 - 0.057273593
Average (Standard dev.)0.00020151319 (0.0020879514)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 238.59999 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0110.0570.000

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Supplemental data

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Sample components

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Entire Drosophila Dicer-2 bound to blunt dsRNA

EntireName: Drosophila Dicer-2 bound to blunt dsRNA / Number of components: 4

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Component #1: protein, Drosophila Dicer-2 bound to blunt dsRNA

ProteinName: Drosophila Dicer-2 bound to blunt dsRNA / Recombinant expression: No
SourceSpecies: Drosophila melanogaster / arthropod / キイロショウジョウバエ /
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #2: protein, Dicer-2, isoform A

ProteinName: Dicer-2, isoform A / Recombinant expression: No
MassTheoretical: 198.074797 kDa
Source (engineered)Expression System: Drosophila melanogaster / arthropod / キイロショウジョウバエ /

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Component #3: nucleic-acid, RNA (5'-R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*U...

Nucleic-acidName: 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')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGAGGUAGUA GGUUGUAUAG UAGUAAGACC AGACCCUAGA CCAAUUCAUG CC
MassTheoretical: 16.781023 kDa

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Component #4: nucleic-acid, RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*C...

Nucleic-acidName: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCAUGAAUU GGUCUAGGGU CUGGUCUUAC UACUAUACAA CCUACUACCU CC
MassTheoretical: 16.528768 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 19445
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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