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- EMDB-2783: siRNA Nanoring -

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Basic information

Entry
Database: EMDB / ID: EMD-2783
TitlesiRNA Nanoring
Map dataReconstruction of siRNA nanoring
Sample
  • Sample: siRNA nanoring
  • RNA: siRNA nanoring
KeywordssiRNA Nanoring / RNA nanotechnology / RNA nanoparticles / RNA interference
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsAfonin 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
CitationJournal: 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
DepositionSep 18, 2014-
Header (metadata) releaseSep 24, 2014-
Map releaseSep 24, 2014-
UpdateOct 15, 2014-
Current statusOct 15, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2783.png

Downloads & links

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Map

FileDownload / File: emd_2783.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of siRNA nanoring
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 300 pix.
= 543. Å		1.81 Å/pix.
x 300 pix.
= 543. Å		1.81 Å/pix.
x 300 pix.
= 543. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-1.48297215 - 5.19088697
Average (Standard dev.)0.00949332 (±0.19490133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 543.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z543.000543.000543.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-1.4835.1910.009

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Supplemental data

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Sample components

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Entire : siRNA nanoring

EntireName: siRNA nanoring
Components
  • Sample: siRNA nanoring
  • RNA: siRNA nanoring

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Supramolecule #1000: siRNA nanoring

SupramoleculeName: siRNA nanoring / type: sample / ID: 1000 / Details: Calculation from sequence / Oligomeric state: 6 / Number unique components: 1
Molecular weightExperimental: 200 KDa / Theoretical: 200 KDa / Method: Calculation from sequence

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Macromolecule #1: siRNA nanoring

MacromoleculeName: siRNA nanoring / type: rna / ID: 1 / Name.synonym: siRNA hexamer / Details: Synthetic RNA sequence / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 200 KDa / Theoretical: 200 KDa
SequenceString:
GGGAACCGUC CACUGGUUCC CGCUACGAGA GCCUGCCUCG UAGCUUCGGU GGUGCAGAUG AACUUCAGGG UCA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8.3 / Details: 89 mM Tris-borate, 2 mM Mg(OAc)2.
GridDetails: Quantifoil Copper 200 mesh R 3.5/1 grids were washed overnight 432 with acetone. Glow discharged.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 90 K / Max: 105 K / Average: 100 K
DateJan 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 500 / Average electron dose: 33 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using EMAN2.
CTF correctionDetails: Frame
Final reconstructionApplied 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 classificationNumber classes: 24

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