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- EMDB-5953: Cryo-electron microscopy of iron-core lacking encapsulin nanocomp... -

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Basic information

Entry
Database: EMDB / ID: EMD-5953
TitleCryo-electron microscopy of iron-core lacking encapsulin nanocompartments from Myxococcus xanthus
Map dataReconstruction from core-lacking encapsulin nanocompartments from Myxococcus xanthus
Sample
  • Sample: Core-lacking nanocompartments purified from Myxococcus xanthus
  • Protein or peptide: EncA
  • Protein or peptide: EncB
  • Protein or peptide: EncC
  • Protein or peptide: EncD
KeywordsFerritin / encapsulin / HK97 fold / cryo electron microscopy / oxidative stress
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein EncA
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsMcHugh CA / Fontana J / Nemecek D / Cheng N / Aksyuk AA / Heymann JB / Winkler DC / Lam AS / Wall JS / Steven AC / Hoiczyk E
CitationJournal: EMBO J / Year: 2014
Title: A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress.
Authors: Colleen A McHugh / Juan Fontana / Daniel Nemecek / Naiqian Cheng / Anastasia A Aksyuk / J Bernard Heymann / Dennis C Winkler / Alan S Lam / Joseph S Wall / Alasdair C Steven / Egbert Hoiczyk /
Abstract: Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound ...Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
History
DepositionApr 30, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 30, 2014-
UpdateSep 10, 2014-
Current statusSep 10, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5953.png

Downloads & links

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Map

FileDownload / File: emd_5953.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction from core-lacking encapsulin nanocompartments from Myxococcus xanthus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.45 Å/pix.
x 256 pix.
= 627.2 Å		2.45 Å/pix.
x 256 pix.
= 627.2 Å		2.45 Å/pix.
x 256 pix.
= 627.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-7.18469906 - 7.87637091
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 627.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.452.452.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z627.200627.200627.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-7.1857.8760.000

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Supplemental data

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Sample components

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Entire : Core-lacking nanocompartments purified from Myxococcus xanthus

EntireName: Core-lacking nanocompartments purified from Myxococcus xanthus
Components
  • Sample: Core-lacking nanocompartments purified from Myxococcus xanthus
  • Protein or peptide: EncA
  • Protein or peptide: EncB
  • Protein or peptide: EncC
  • Protein or peptide: EncD

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Supramolecule #1000: Core-lacking nanocompartments purified from Myxococcus xanthus

SupramoleculeName: Core-lacking nanocompartments purified from Myxococcus xanthus
type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 4

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Macromolecule #1: EncA

MacromoleculeName: EncA / type: protein_or_peptide / ID: 1 / Name.synonym: Encapsulin nanocompartment, MXAN_3556 / Details: Major component, forms the shell. / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622

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Macromolecule #2: EncB

MacromoleculeName: EncB / type: protein_or_peptide / ID: 2 / Name.synonym: Encapsulin nanocompartment, MXAN_3557 / Details: Located inside shell / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622

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Macromolecule #3: EncC

MacromoleculeName: EncC / type: protein_or_peptide / ID: 3 / Name.synonym: Encapsulin nanocompartment, MXAN_4464 / Details: Located inside shell / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622

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Macromolecule #4: EncD

MacromoleculeName: EncD / type: protein_or_peptide / ID: 4 / Name.synonym: Encapsulin nanocompartment, MXAN_2410 / Details: Located inside shell / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622

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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

Concentration0.1 mg/mL
BufferpH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2
GridDetails: 400 mesh carbon grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber temperature: 83 K / Instrument: LEICA KF80

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateAug 23, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 61 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51840 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsBsoft package was used.
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: Bsoft / Number images used: 400
Final two d classificationNumber classes: 1
FSC plot (resolution estimation)

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