Journal: 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
Deposition
Jul 5, 2017
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Header (metadata) release
Aug 16, 2017
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Map release
Oct 18, 2017
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Update
Nov 29, 2023
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Current status
Nov 29, 2023
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)
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Map
File
Download / File: emd_3781.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Bioorigami coiled-coil tetrahedron TET12SN.
Voxel size
X=Y=Z: 2.84 Å
Density
Contour Level
By AUTHOR: 0.0559 / Movie #1: 0.0559
Minimum - Maximum
-0.047377944 - 0.25644943
Average (Standard dev.)
0.0002109636 (±0.013649056)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
100
100
100
Spacing
100
100
100
Cell
A=B=C: 284.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.84
2.84
2.84
M x/y/z
100
100
100
origin x/y/z
0.000
0.000
0.000
length x/y/z
284.000
284.000
284.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
280
280
280
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
100
100
100
D min/max/mean
-0.047
0.256
0.000
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Supplemental data
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Sample components
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Entire : TET12SN
Entire
Name: TET12SN
Components
Complex: TET12SN
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Supramolecule #1: TET12SN
Supramolecule
Name: TET12SN / type: complex / ID: 1 / Parent: 0 Details: Coiled coil single chain protein origami tetrahedron 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
Method
negative staining
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.03 mg/mL
Buffer
pH: 7.5 Component:
Concentration
Name
Formula
20.0 mM
Tris
150.0 mM
Sodium Cloride
NaCl
10.0 %
Glycerol
Staining
Type: 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
Microscope
JEOL 1230
Image recording
Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 15.0 e/Å2
Electron beam
Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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Image processing
Startup model
Type of model: OTHER
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Xmipp, RELION) / Number images used: 13425
Initial angle assignment
Type: PROJECTION MATCHING
Final angle assignment
Type: PROJECTION MATCHING
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