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- EMDB-3788: PYR16SN density map (Design of in vivo self-assembling coiled-coi... -

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Basic information

Entry
Database: EMDB / ID: EMD-3788
TitlePYR16SN density map (Design of in vivo self-assembling coiled-coil protein origami)
Map dataPyr16 SN density map (Design of in vivo self-assembling coiled-coil protein origami )
Sample
  • Complex: TET16SN
Biological speciesDesigned protein (others)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 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: 0.0487
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0487
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_3788.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPyr16 SN density map (Design of in vivo self-assembling coiled-coil protein origami )
Voxel sizeX=Y=Z: 2.84 Å
Density
Contour LevelBy AUTHOR: 0.0487 / Movie #1: 0.0487
Minimum - Maximum-0.057944752 - 0.20514989
Average (Standard dev.)0.00010410141 (±0.010486634)
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-0.0580.2050.000

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Supplemental data

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Sample components

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Entire : TET16SN

EntireName: TET16SN
Components
  • Complex: TET16SN

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Supramolecule #1: TET16SN

SupramoleculeName: TET16SN / type: complex / ID: 1 / Parent: 0
Details: Coiled coil single chain protein origami pyramid 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 ClorideNaClSodium chloride
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
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 15.0 e/Å2

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Xmipp, RELION) / Number images used: 18251

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