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- EMDB-3608: Non-loaded encapsulin particles with icosahedral symmetry -

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Basic information

Entry
Database: EMDB / ID: 3608
TitleNon-loaded encapsulin particles with icosahedral symmetry
Map data
SampleNon-loaded encapsulin:
SourceBrevibacterium linens (bacteria)
Methodsingle particle reconstruction / cryo EM / 11.4 Å resolution
AuthorsPutri RM / Allende-Ballestero C / Luque D / Klem R / Rousou AA / Liu A / Traulsen CH / Rurup WF / Koay MST / Caston JR / Cornelissen JJLM
CitationJournal: ACS Nano / Year: 2017
Title: Structural Characterization of Native and Modified Encapsulins as Nanoplatforms for in Vitro Catalysis and Cellular Uptake.
Authors: Rindia M Putri / Carolina Allende-Ballestero / Daniel Luque / Robin Klem / Katerina-Asteria Rousou / Aijie Liu / Christoph H-H Traulsen / W Frederik Rurup / Melissa S T Koay / José R Castón / Jeroen J L M Cornelissen
DateDeposition: Feb 28, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Dec 13, 2017 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3608.map.gz (map file in CCP4 format, 1756 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
76 pix
4.32 Å/pix.
= 328.32 Å
76 pix
4.32 Å/pix.
= 328.32 Å
76 pix
4.32 Å/pix.
= 328.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.32 Å
Density
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum-0.24877 - 0.74012
Average (Standard dev.)0.023396458 (0.1040529)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions767676
Origin-38-38-38
Limit373737
Spacing767676
CellA=B=C: 328.32 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.324.324.32
M x/y/z767676
origin x/y/z0.0000.0000.000
length x/y/z328.320328.320328.320
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-38-38-38
NC/NR/NS767676
D min/max/mean-0.2490.7400.023

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Supplemental data

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Sample components

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Entire Non-loaded encapsulin

EntireName: Non-loaded encapsulin / Details: Non-Loaded Brevibacterium linens encapsulin / Number of components: 1
MassTheoretical: 2 MDa

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Component #1: cellular-component, Non-loaded encapsulin

Cellular-componentName: Non-loaded encapsulin / Details: Non-Loaded Brevibacterium linens encapsulin / Recombinant expression: No
MassTheoretical: 2 MDa
SourceSpecies: Brevibacterium linens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 20 mM Tris-Cl pH 7.5, 150 mM NH4Cl, 1 mM betamercaptoethanol
pH: 7.5
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI EAGLE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 192 / Sampling size: 15 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 4246
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 11.4 Å / Resolution method: FSC 0.5 CUT-OFF

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