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- EMDB-24824: Nanosandwich composite of two RNA-DNA hybrid nanotriangles bound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-24824
TitleNanosandwich composite of two RNA-DNA hybrid nanotriangles bound at a streptavidin core
Map dataNano-sandwich composite consisting of two RNA-DNA hybrid nanotriangles bound to a streptavidin core.
Sample
  • Complex: Sandwich complex of two RNA-DNA hybrid nanotriangles bound at a streptavidin core
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsHermann T / Chen S / Xing L / Zhang D / Monferrer A
Funding support1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2104335
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid.
Authors: Shi Chen / Li Xing / Douglas Zhang / Alba Monferrer / Thomas Hermann /
Abstract: Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural ...Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural biomolecules. We report the design and kinetically controlled stepwise synthesis of a nano-sandwich composite by programmed noncovalent association of protein, DNA and RNA modules. A homo-tetramer protein core was introduced to control the self-assembly and precise positioning of two RNA-DNA hybrid nanotriangles in a co-parallel sandwich arrangement. Kinetically favored self-assembly of the circularly closed nanostructures at the protein was driven by the intrinsic fast folding ability of RNA corner modules which were added to precursor complex of DNA bound to the protein. The 3D architecture of this first synthetic protein-RNA-DNA complex was confirmed by fluorescence labeling and cryo-electron microscopy studies. The synthesis strategy for the nano-sandwich composite provides a general blueprint for controlled noncovalent assembly of complex supramolecular architectures from protein, DNA and RNA components, which expand the design repertoire for bottom-up preparation of layered biomaterials.
History
DepositionSep 6, 2021-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24824.png

Downloads & links

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Map

FileDownload / File: emd_24824.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNano-sandwich composite consisting of two RNA-DNA hybrid nanotriangles bound to a streptavidin core.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 150 pix.
= 420. Å		2.8 Å/pix.
x 150 pix.
= 420. Å		2.8 Å/pix.
x 150 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.9017164 - 8.548169
Average (Standard dev.)-0.0007223669 (±0.20987366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-1.9028.548-0.001

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Supplemental data

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Sample components

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Entire : Sandwich complex of two RNA-DNA hybrid nanotriangles bound at a s...

EntireName: Sandwich complex of two RNA-DNA hybrid nanotriangles bound at a streptavidin core
Components
  • Complex: Sandwich complex of two RNA-DNA hybrid nanotriangles bound at a streptavidin core

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Supramolecule #1: Sandwich complex of two RNA-DNA hybrid nanotriangles bound at a s...

SupramoleculeName: Sandwich complex of two RNA-DNA hybrid nanotriangles bound at a streptavidin core
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)

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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: 7 / Component - Concentration: 10.0 mM / Component - Name: HEPES
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: PROPANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: OTHER / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

DetailsGatan OneView CCD
Particle selectionNumber selected: 40764
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 6872
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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