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- EMDB-3789: TRIP18SN density map (Design of in vivo self-assembling coiled-co... -

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Basic information

Entry
Database: EMDB / ID: EMD-3789
TitleTRIP18SN density map (Design of in vivo self-assembling coiled-coil protein origami)
Map dataTRIP18SN density map (Design of in vivo self-assembling coiled-coil protein origami)
Sample
  • Complex: TRIP18SN
Biological speciesDesigned protein (others)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsMelero R / Carazo JM
CitationJournal: Nat Biotechnol / Year: 2017
Title: Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.
Authors: Ajasja Ljubetič / Fabio Lapenta / Helena Gradišar / Igor Drobnak / Jana Aupič / Žiga Strmšek / Duško Lainšček / Iva Hafner-Bratkovič / Andreja Majerle / Nuša Krivec / Mojca ...Authors: Ajasja Ljubetič / Fabio Lapenta / Helena Gradišar / Igor Drobnak / Jana Aupič / Žiga Strmšek / Duško Lainšček / Iva Hafner-Bratkovič / Andreja Majerle / Nuša Krivec / Mojca Benčina / Tomaž Pisanski / Tanja Ćirković Veličković / Adam Round / José María Carazo / Roberto Melero / Roman Jerala /
Abstract: Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which ...Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter. Their stability and folding kinetics were similar to those of natural proteins. Solution small-angle X-ray scattering (SAXS), electron microscopy (EM), and biophysical analysis confirmed agreement of the expressed structures with the designs. We also demonstrated self-assembly of a tetrahedral structure in bacteria, mammalian cells, and mice without evidence of inflammation. A semi-automated computational design platform and a toolbox of CC building modules are provided to enable the design of protein cages in any polyhedral shape.
History
DepositionJul 7, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseOct 18, 2017-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0583
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0583
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3789.png

Downloads & links

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Map

FileDownload / File: emd_3789.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRIP18SN density map (Design of in vivo self-assembling coiled-coil protein origami)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.84 Å/pix.
x 100 pix.
= 284. Å		2.84 Å/pix.
x 100 pix.
= 284. Å		2.84 Å/pix.
x 100 pix.
= 284. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0583 / Movie #1: 0.0583
Minimum - Maximum-0.05791028 - 0.23841219
Average (Standard dev.)0.0004877246 (±0.011896608)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 284.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.842.842.84
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z284.000284.000284.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0580.2380.000

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Supplemental data

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Sample components

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Entire : TRIP18SN

EntireName: TRIP18SN
Components
  • Complex: TRIP18SN

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Supramolecule #1: TRIP18SN

SupramoleculeName: TRIP18SN / type: complex / ID: 1 / Parent: 0
Details: Coiled coil single chain protein origami triangular prism composed of soluble dimeric coiled coil segments.
Source (natural)Organism: Designed protein (others)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMSodium ClorideNaCl
10.0 %Glycerol
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: Samples were applied to glow discharged carbon-coated copper grids, washed quickly with distilled water and negatively stained with 2% (w/v) uranyl acetate.

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Electron microscopy

MicroscopeJEOL 1230
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Xmipp, RELION) / Number images used: 15145
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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