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- EMDB-3781: TET12SN density map (Design of in vivo self-assembling coiled-coi... -

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Basic information

Entry
Database: EMDB / ID: 3781
TitleTET12SN density map (Design of in vivo self-assembling coiled-coil protein origami)
Map dataBioorigami coiled-coil tetrahedron TET12SN.
SampleTET12SN:
SourceDesigned protein (others)
Methodsingle particle reconstruction / negative staining / 28 Å resolution
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 Benčina / Tomaž Pisanski / Tanja Ćirković Veličković / Adam Round / José María Carazo / Roberto Melero / Roman Jerala
DateDeposition: Jul 5, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Oct 18, 2017 / Last update: Feb 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0559
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0559
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3781.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.84 Å/pix.
= 284. Å
100 pix
2.84 Å/pix.
= 284. Å
100 pix
2.84 Å/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
Contour Level:0.0559 (by author), 0.0559 (movie #1):
Minimum - Maximum-0.047377944 - 0.25644943
Average (Standard dev.)0.0002109636 (0.013649056)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin0.00.00.0
Limit99.099.099.0
Spacing100100100
CellA=B=C: 284.0 Å
α=β=γ: 90.0 deg.

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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0470.2560.000

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Supplemental data

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Sample components

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Entire TET12SN

EntireName: TET12SN
Details: Coiled coil single chain protein origami tetrahedron composed of soluble dimeric coiled coil segments.
Number of components: 1

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Component #1: protein, TET12SN

ProteinName: TET12SN
Details: Coiled coil single chain protein origami tetrahedron composed of soluble dimeric coiled coil segments.
Recombinant expression: No
SourceSpecies: Designed protein (others)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET-41a / Strain: NiCo21(DE3)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.03 mg/ml / pH: 7.5
StainingSamples were applied to glow discharged carbon-coated copper grids, washed quickly with distilled water and negatively stained with 2% (w/v) uranyl acetate.
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 1230
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 13425
3D reconstructionSoftware: Xmipp, RELION / Resolution: 28 Å / Resolution method: FSC 0.143 CUT-OFF

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