+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2783 | |||||||||
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Title | siRNA Nanoring | |||||||||
Map data | Reconstruction of siRNA nanoring | |||||||||
Sample |
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Keywords | siRNA Nanoring / RNA nanotechnology / RNA nanoparticles / RNA interference | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
Authors | Afonin KA / Viard M / Koyfman AY / Martins AN / Kasprzak WK / Panigaj M / Desai R / Santhanam A / Grabow WW / Jaeger L ...Afonin KA / Viard M / Koyfman AY / Martins AN / Kasprzak WK / Panigaj M / Desai R / Santhanam A / Grabow WW / Jaeger L / Heldman E / Reiser J / Chiu W / Freed EO / Shapiro BA | |||||||||
Citation | Journal: Nano Lett / Year: 2014 Title: Multifunctional RNA nanoparticles. Authors: Kirill A Afonin / Mathias Viard / Alexey Y Koyfman / Angelica N Martins / Wojciech K Kasprzak / Martin Panigaj / Ravi Desai / Arti Santhanam / Wade W Grabow / Luc Jaeger / Eliahu Heldman / ...Authors: Kirill A Afonin / Mathias Viard / Alexey Y Koyfman / Angelica N Martins / Wojciech K Kasprzak / Martin Panigaj / Ravi Desai / Arti Santhanam / Wade W Grabow / Luc Jaeger / Eliahu Heldman / Jakob Reiser / Wah Chiu / Eric O Freed / Bruce A Shapiro / Abstract: Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, ...Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, besides functionalization with multiple different short interfering RNAs for combinatorial RNA interference (e.g., against multiple HIV-1 genes), nanorings also allow simultaneous embedment of assorted RNA aptamers, fluorescent dyes, proteins, as well as recently developed RNA-DNA hybrids aimed to conditionally activate multiple split functionalities inside cells. | |||||||||
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_2783.map.gz | 92.6 MB | EMDB map data format | |
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Header (meta data) | emd-2783-v30.xml emd-2783.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | EMD-2783.png | 99.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2783 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2783 | HTTPS FTP |
-Validation report
Summary document | emd_2783_validation.pdf.gz | 181.7 KB | Display | EMDB validaton report |
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Full document | emd_2783_full_validation.pdf.gz | 180.8 KB | Display | |
Data in XML | emd_2783_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2783 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2783 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2783.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of siRNA nanoring | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.81 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 : siRNA nanoring
Entire | Name: siRNA nanoring |
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Components |
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-Supramolecule #1000: siRNA nanoring
Supramolecule | Name: siRNA nanoring / type: sample / ID: 1000 / Details: Calculation from sequence / Oligomeric state: 6 / Number unique components: 1 |
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Molecular weight | Experimental: 200 KDa / Theoretical: 200 KDa / Method: Calculation from sequence |
-Macromolecule #1: siRNA nanoring
Macromolecule | Name: siRNA nanoring / type: rna / ID: 1 / Name.synonym: siRNA hexamer / Details: Synthetic RNA sequence / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Experimental: 200 KDa / Theoretical: 200 KDa |
Sequence | String: GGGAACCGUC CACUGGUUCC CGCUACGAGA GCCUGCCUCG UAGCUUCGGU GGUGCAGAUG AACUUCAGGG UCA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8.3 / Details: 89 mM Tris-borate, 2 mM Mg(OAc)2. |
Grid | Details: Quantifoil Copper 200 mesh R 3.5/1 grids were washed overnight 432 with acetone. Glow discharged. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III / Method: Blot for 1 second before plunging |
-Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 90 K / Max: 105 K / Average: 100 K |
Date | Jan 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 500 / Average electron dose: 33 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 83555 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected using EMAN2. |
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CTF correction | Details: Frame |
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 11067 |
Final two d classification | Number classes: 24 |