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- EMDB-3612: DyP Encapsulin particle with imposed icosahedral symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-3612
TitleDyP Encapsulin particle with imposed icosahedral symmetry
Map dataDyP Encapsulin particle with imposed icosahedral symmetry
Sample
  • Organelle or cellular component: DyP encapsulin
Biological speciesBrevibacterium linens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.1 Å
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 ...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 /
Abstract: Recent years have witnessed the emergence of bacterial semiorganelle encapsulins as promising platforms for bio-nanotechnology. To advance the development of encapsulins as nanoplatforms, a ...Recent years have witnessed the emergence of bacterial semiorganelle encapsulins as promising platforms for bio-nanotechnology. To advance the development of encapsulins as nanoplatforms, a functional and structural basis of these assemblies is required. Encapsulin from Brevibacterium linens is known to be a protein-based vessel for an enzyme cargo in its cavity, which could be replaced with a foreign cargo, resulting in a modified encapsulin. Here, we characterize the native structure of B. linens encapsulins with both native and foreign cargo using cryo-electron microscopy (cryo-EM). Furthermore, by harnessing the confined enzyme (i.e., a peroxidase), we demonstrate the functionality of the encapsulin for an in vitro surface-immobilized catalysis in a cascade pathway with an additional enzyme, glucose oxidase. We also demonstrate the in vivo functionality of the encapsulin for cellular uptake using mammalian macrophages. Unraveling both the structure and functionality of the encapsulins allows transforming biological nanocompartments into functional systems.
History
DepositionMar 3, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseDec 13, 2017-
UpdateJan 10, 2018-
Current statusJan 10, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3612.png

Downloads & links

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Map

FileDownload / File: emd_3612.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDyP Encapsulin particle with imposed icosahedral symmetry
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.210581 - 0.473054
Average (Standard dev.)0.019766685 (±0.079974204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-38-38-38
Dimensions767676
Spacing767676
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS-38-38-38
NC/NR/NS767676
D min/max/mean-0.2110.4730.020

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Supplemental data

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Sample components

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Entire : DyP encapsulin

EntireName: DyP encapsulin
Components
  • Organelle or cellular component: DyP encapsulin

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Supramolecule #1: DyP encapsulin

SupramoleculeName: DyP encapsulin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Brevibacterium linens encapsulin loaded with DyP
Source (natural)Organism: Brevibacterium linens (bacteria)
Molecular weightTheoretical: 2 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Details: 20 mM Tris-Cl pH 7.5, 150 mM NH4Cl, 1 mM betamercaptoethanol
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.0 µm / Number grids imaged: 1 / Number real images: 141 / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.2 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19591
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3dkt

Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 12833
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 12833 / Software - Name: RELION (ver. 2.0)

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