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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1530 | |||||||||
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Title | Structure of hexameric DyP from Brevibacterium linens | |||||||||
![]() | Structure of hexameric DyP from Brevibacterium linens | |||||||||
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![]() | protein complex / hexamer / peroxidase / dye-decolorizing peroxidase / heme containing peroxidase | |||||||||
Function / homology | Dyp-type peroxidase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.0 Å | |||||||||
![]() | Sutter M / Boehringer D / Gutmann S / Gunther S / Prangishvili D / Loessner MJ / Stetter KO / Weber-Ban E / Ban N | |||||||||
![]() | ![]() Title: Structural basis of enzyme encapsulation into a bacterial nanocompartment. Authors: Markus Sutter / Daniel Boehringer / Sascha Gutmann / Susanne Günther / David Prangishvili / Martin J Loessner / Karl O Stetter / Eilika Weber-Ban / Nenad Ban / ![]() Abstract: Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular ...Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood. Here we show, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-angstroms resolution reveals that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 angstroms. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 623.7 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.9 KB 8.9 KB | Display Display | ![]() |
Images | ![]() | 68.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 205.8 KB | Display | ![]() |
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Full document | ![]() | 204.9 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Structure of hexameric DyP from Brevibacterium linens | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Structure of hexameric DyP from Brevibacterium linens
Entire | Name: Structure of hexameric DyP from Brevibacterium linens |
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Components |
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-Supramolecule #1000: Structure of hexameric DyP from Brevibacterium linens
Supramolecule | Name: Structure of hexameric DyP from Brevibacterium linens / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: hexamer / Number unique components: 1 |
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Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: dye-decolorizing peroxidase
Macromolecule | Name: dye-decolorizing peroxidase / type: protein_or_peptide / ID: 1 / Name.synonym: Dyp / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40 KDa |
Recombinant expression | Organism: Escherichia coli Rosetta / Recombinant plasmid: pET21a |
Sequence | InterPro: Dyp-type peroxidase |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Staining | Type: NEGATIVE / Details: 2% w/v uranyl acetate |
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Grid | Details: carbon coated 200 mesh copper grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Average: 295 K |
Specialist optics | Energy filter - Name: Tridiem Gatan |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Digitization - Sampling interval: 1.4 µm / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
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Image processing
CTF correction | Details: Each image |
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Final reconstruction | Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: IMAGIC-5 / Number images used: 2878 |