+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8366 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 5 nm RNA nanoprism | |||||||||
Map data | 5 nm RNA nanoprism | |||||||||
Sample |
| |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 22.0 Å | |||||||||
Authors | Khisamutdinov E / Jasinski D / Li H / Zhang K / Chiu W / Guo P | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Adv Mater / Year: 2016 Title: Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs. Authors: Emil F Khisamutdinov / Daniel L Jasinski / Hui Li / Kaiming Zhang / Wah Chiu / Peixuan Guo / Abstract: Constructing containers with defined shape and size to load and protect therapeutics and subsequently control their release in the human body has long been a dream. The fabrication of 3D RNA prisms, ...Constructing containers with defined shape and size to load and protect therapeutics and subsequently control their release in the human body has long been a dream. The fabrication of 3D RNA prisms, characterized by atomic force microscopy, cryo-electron microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis, is reported for the loading and protection of small molecules, proteins, small RNA molecules, and their controlled release. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8366.map.gz | 6.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8366-v30.xml emd-8366.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_8366.png | 25.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8366 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8366 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_8366.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 5 nm RNA nanoprism | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : 5 nm RNA prism
Entire | Name: 5 nm RNA prism |
---|---|
Components |
|
-Supramolecule #1: 5 nm RNA prism
Supramolecule | Name: 5 nm RNA prism / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The RNA strands are made by in vitro transcription. |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Experimental: 110 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
---|---|
Buffer | pH: 8 / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride / Details: 100 mM NaCl, 50 mM Tris , 10 mM MgCl2 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).. |
Details | The RNA strands are made by in vitro transcription. |
-Electron microscopy
Microscope | JEOL 2200FS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Detector mode: OTHER / Number real images: 30 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2 |
-Image processing
Particle selection | Number selected: 2340 |
---|---|
CTF correction | Software - Name: EMAN (ver. 2.1) |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: COMMON LINE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.1) |