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- EMDB-1530: Structure of hexameric DyP from Brevibacterium linens -

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Basic information

Entry
Database: EMDB / ID: EMD-1530
TitleStructure of hexameric DyP from Brevibacterium linens
Map dataStructure of hexameric DyP from Brevibacterium linens
Sample
  • Sample: Structure of hexameric DyP from Brevibacterium linens
  • Protein or peptide: dye-decolorizing peroxidase
Keywordsprotein complex / hexamer / peroxidase / dye-decolorizing peroxidase / heme containing peroxidase
Function / homologyDyp-type peroxidase
Function and homology information
Biological speciesBrevibacterium linens (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 16.0 Å
AuthorsSutter M / Boehringer D / Gutmann S / Gunther S / Prangishvili D / Loessner MJ / Stetter KO / Weber-Ban E / Ban N
CitationJournal: Nat Struct Mol Biol / Year: 2008
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
DepositionJun 24, 2008-
Header (metadata) releaseJun 24, 2008-
Map releaseJun 11, 2009-
UpdateAug 31, 2011-
Current statusAug 31, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1530.gif

Downloads & links

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Map

FileDownload / File: emd_1530.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of hexameric DyP from Brevibacterium linens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 64 pix.
= 179.2 Å		2.8 Å/pix.
x 64 pix.
= 179.2 Å		2.8 Å/pix.
x 64 pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.18
Minimum - Maximum-1.38813 - 0.944775
Average (Standard dev.)-0.00162246 (±0.125636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-31-32
Dimensions646464
Spacing646464
CellA=B=C: 179.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS-31-32-32
NC/NR/NS646464
D min/max/mean-1.3880.945-0.002

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Supplemental data

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Sample components

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Entire : Structure of hexameric DyP from Brevibacterium linens

EntireName: Structure of hexameric DyP from Brevibacterium linens
Components
  • Sample: Structure of hexameric DyP from Brevibacterium linens
  • Protein or peptide: dye-decolorizing peroxidase

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Supramolecule #1000: Structure of hexameric DyP from Brevibacterium linens

SupramoleculeName: Structure of hexameric DyP from Brevibacterium linens / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: hexamer / Number unique components: 1
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: dye-decolorizing peroxidase

MacromoleculeName: dye-decolorizing peroxidase / type: protein_or_peptide / ID: 1 / Name.synonym: Dyp / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Brevibacterium linens (bacteria) / Strain: M18
Molecular weightTheoretical: 40 KDa
Recombinant expressionOrganism: Escherichia coli Rosetta / Recombinant plasmid: pET21a
SequenceInterPro: Dyp-type peroxidase

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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

StainingType: NEGATIVE / Details: 2% w/v uranyl acetate
GridDetails: carbon coated 200 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 295 K
Specialist opticsEnergy filter - Name: Tridiem Gatan
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Digitization - Sampling interval: 1.4 µm / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: Each image
Final reconstructionApplied 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

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