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- EMDB-7291: Drosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RN... -

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Basic information

Database: EMDB / ID: 7291
TitleDrosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RNaseIII domains)
SampleDrosophila Dicer-2 (apo)
SourceDrosophila melanogaster / arthropod / /
Map dataDrosophila Dicer-2 (apo)
Methodsingle particle reconstruction, at 7.1 Å resolution
AuthorsShen PS / Sinha NK
CitationScience, 2018, 359, 329-334

Science, 2018, 359, 329-334 Yorodumi Papers
Dicer uses distinct modules for recognizing dsRNA termini.
Niladri K Sinha / Janet Iwasa / Peter S Shen / Brenda L Bass

Validation ReportPDB-ID: 6bua

SummaryFull reportAbout validation report
DateDeposition: Dec 9, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Jan 31, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bua
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_7291.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.19 Å/pix.
= 305.408 Å
256 pix
1.19 Å/pix.
= 305.408 Å
256 pix
1.19 Å/pix.
= 305.408 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.193 Å
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.0038245027 - 0.030697713
Average (Standard dev.)-3.1299314E-5 (0.0012950517)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 305.408 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1931.1931.193
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z305.408305.408305.408
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0040.031-0.000

Supplemental data

Sample components

Entire Drosophila Dicer-2 (apo)

EntireName: Drosophila Dicer-2 (apo) / Number of components: 2

Component #1: protein, Drosophila Dicer-2 (apo)

ProteinName: Drosophila Dicer-2 (apo) / Recombinant expression: No
SourceSpecies: Drosophila melanogaster / arthropod / /
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Fall armyworm

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 / /

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
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)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 85119
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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