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- EMDB-20697: RNA X with 24 PTX -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-20697
TitleRNA X with 24 PTX
Map dataRNA X with 24 PTX
Sample
  • Complex: Designed RNA X nanoparticle with 24 PTX (paclitaxel)
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsZhang K / Guo S / Chiu W
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteP41GM103832 United States
National Institutes of Health/National Human Genome Research InstituteU54GM103297 United States
CitationJournal: Nat Commun / Year: 2020
Title: Ultra-thermostable RNA nanoparticles for solubilizing and high-yield loading of paclitaxel for breast cancer therapy.
Authors: Sijin Guo / Mario Vieweger / Kaiming Zhang / Hongran Yin / Hongzhi Wang / Xin Li / Shanshan Li / Shuiying Hu / Alex Sparreboom / B Mark Evers / Yizhou Dong / Wah Chiu / Peixuan Guo /
Abstract: Paclitaxel is widely used in cancer treatments, but poor water-solubility and toxicity raise serious concerns. Here we report an RNA four-way junction nanoparticle with ultra-thermodynamic stability ...Paclitaxel is widely used in cancer treatments, but poor water-solubility and toxicity raise serious concerns. Here we report an RNA four-way junction nanoparticle with ultra-thermodynamic stability to solubilize and load paclitaxel for targeted cancer therapy. Each RNA nanoparticle covalently loads twenty-four paclitaxel molecules as a prodrug. The RNA-paclitaxel complex is structurally rigid and stable, demonstrated by the sub-nanometer resolution imaging of cryo-EM. Using RNA nanoparticles as carriers increases the water-solubility of paclitaxel by 32,000-fold. Intravenous injections of RNA-paclitaxel nanoparticles with specific cancer-targeting ligand dramatically inhibit breast cancer growth, with nearly undetectable toxicity and immune responses in mice. No fatalities are observed at a paclitaxel dose equal to the reported LD. The use of ultra-thermostable RNA nanoparticles to deliver chemical prodrugs addresses issues with RNA unfolding and nanoparticle dissociation after high-density drug loading. This finding provides a stable nano-platform for chemo-drug delivery as well as an efficient method to solubilize hydrophobic drugs.
History
DepositionSep 8, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseMar 4, 2020-
UpdateMar 4, 2020-
Current statusMar 4, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.601
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.601
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20697.png

Downloads & links

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Map

FileDownload / File: emd_20697.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA X with 24 PTX
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 224 pix.
= 237.44 Å		1.06 Å/pix.
x 224 pix.
= 237.44 Å		1.06 Å/pix.
x 224 pix.
= 237.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.601 / Movie #1: 0.601
Minimum - Maximum-0.68120897 - 1.7923456
Average (Standard dev.)0.0036986612 (±0.07707173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 237.43999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z237.440237.440237.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.6811.7920.004

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Supplemental data

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Sample components

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Entire : Designed RNA X nanoparticle with 24 PTX (paclitaxel)

EntireName: Designed RNA X nanoparticle with 24 PTX (paclitaxel)
Components
  • Complex: Designed RNA X nanoparticle with 24 PTX (paclitaxel)

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Supramolecule #1: Designed RNA X nanoparticle with 24 PTX (paclitaxel)

SupramoleculeName: Designed RNA X nanoparticle with 24 PTX (paclitaxel) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: unidentified (others)
Molecular weightExperimental: 60 KDa

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 3800 / Average exposure time: 6.0 sec. / Average electron dose: 45.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 406408
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 125909
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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