+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15299 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mouse endoribonuclease Dicer | |||||||||
Map data | Locally refined electron density map of Dicer helicase domain | |||||||||
Sample |
| |||||||||
Keywords | endoribonuclease / gene silencing / post-transcriptional / catalytic enzyme / cytoplasm / RNA BINDING PROTEIN | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.18 Å | |||||||||
Authors | Zanova M / Zapletal D / Kubicek K / Stefl R / Pinkas M / Novacek J | |||||||||
Funding support | Czech Republic, 2 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_15299.map.gz | 200.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-15299-v30.xml emd-15299.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15299_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_15299.png | 60.4 KB | ||
Others | emd_15299_half_map_1.map.gz emd_15299_half_map_2.map.gz | 177.1 MB 177.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15299 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15299 | HTTPS FTP |
-Validation report
Summary document | emd_15299_validation.pdf.gz | 684.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_15299_full_validation.pdf.gz | 684.4 KB | Display | |
Data in XML | emd_15299_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_15299_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15299 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15299 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_15299.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Locally refined electron density map of Dicer helicase domain | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: half map A
File | emd_15299_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map B
File | emd_15299_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Free form of mouse somatic dicer
Entire | Name: Free form of mouse somatic dicer |
---|---|
Components |
|
-Supramolecule #1: Free form of mouse somatic dicer
Supramolecule | Name: 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) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.20 mg/mL | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
Details: The buffer was always prepared fresh | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Described in STAR methods. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6354 / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
+Image processing
-Atomic model buiding 1
Details | Endoribonuclease 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. |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 Target criteria: Ramachandran Plot, Rotamer Analysis, Density Analysis |
-Atomic model buiding 2
Details | PHENIX Real-space refinement was used for flexible fitting. |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 / Target criteria: Correlation coefficient |
-Atomic model buiding 3
Details | ISOLDE was used for flexible fitting with defined torsion restraints |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 Target criteria: Ramachandran Plot, Rotamer Analysis, Clash Score |