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- EMDB-11831: BIP18SN. De novo coiled-coil-based bipyramidal protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-11831
TitleBIP18SN. De novo coiled-coil-based bipyramidal protein
Map dataCoiled coil single chain protein origami bipyramid composed of dimeric coiled coil segments.
Sample
  • Complex: Coiled-coil-based protein monomer
Keywordscoiled coil protein origami / DE NOVO PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLapenta F / Aupic J / Vezzoli M / Strmsek Z / Da Vela S / Svergun DI / Melero R / Carazo JM / Jerala R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)787115European Union
CitationJournal: Nat Commun / Year: 2021
Title: Self-assembly and regulation of protein cages from pre-organised coiled-coil modules.
Authors: Fabio Lapenta / Jana Aupič / Marco Vezzoli / Žiga Strmšek / Stefano Da Vela / Dmitri I Svergun / José María Carazo / Roberto Melero / Roman Jerala /
Abstract: Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil ...Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.
History
DepositionOct 12, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
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: 0.0517
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0517
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11831.png

Downloads & links

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Map

FileDownload / File: emd_11831.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoiled coil single chain protein origami bipyramid composed of dimeric coiled coil segments.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 100 pix.
= 100. Å		1 Å/pix.
x 100 pix.
= 100. Å		1 Å/pix.
x 100 pix.
= 100. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0517 / Movie #1: 0.0517
Minimum - Maximum-0.044970453 - 0.19019175
Average (Standard dev.)-0.00035193146 (±0.010752927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 100.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z100.000100.000100.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0450.190-0.000

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Supplemental data

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Sample components

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Entire : Coiled-coil-based protein monomer

EntireName: Coiled-coil-based protein monomer
Components
  • Complex: Coiled-coil-based protein monomer

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Supramolecule #1: Coiled-coil-based protein monomer

SupramoleculeName: Coiled-coil-based protein monomer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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
StainingType: NEGATIVE / Material: uranyl acetate
DetailsSamples 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-F415 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 54926 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: JEOL

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Xmipp

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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