+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8233 | |||||||||
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Title | 8 nm RNA Tetrahedron | |||||||||
Map data | RNA 8 nm Tetrahedron | |||||||||
Sample |
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Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Li H / Zhang K / Pi F / Guo S / Shlyakhtenko L / Chiu W / Shu D / Guo P | |||||||||
Citation | Journal: Adv Mater / Year: 2016 Title: Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. Authors: Hui Li / Kaiming Zhang / Fengmei Pi / Sijin Guo / Luda Shlyakhtenko / Wah Chiu / Dan Shu / Peixuan Guo / Abstract: RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be ...RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be extended to construct higher-order polyhedral RNA architectures for various applications such as targeted cancer imaging and therapy. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8233.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-8233-v30.xml emd-8233.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_8233.png | 90.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8233 | HTTPS FTP |
-Validation report
Summary document | emd_8233_validation.pdf.gz | 328.4 KB | Display | EMDB validaton report |
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Full document | emd_8233_full_validation.pdf.gz | 327.9 KB | Display | |
Data in XML | emd_8233_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_8233_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8233 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8233.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNA 8 nm Tetrahedron | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 8 nm RNA Tetrahedron
Entire | Name: 8 nm RNA Tetrahedron |
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Components |
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-Supramolecule #1: 8 nm RNA Tetrahedron
Supramolecule | Name: 8 nm RNA Tetrahedron / type: complex / ID: 1 / Parent: 0 Details: The RNA strands are made by in vitro transcription. |
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Molecular weight | Theoretical: 120 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8 / Details: 100 mM NaCl, 50 mM Tris |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Blot for 1.5 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 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 52 / Average exposure time: 1.5 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |