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Yorodumi- EMDB-5953: Cryo-electron microscopy of iron-core lacking encapsulin nanocomp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5953 | |||||||||
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Title | Cryo-electron microscopy of iron-core lacking encapsulin nanocompartments from Myxococcus xanthus | |||||||||
Map data | Reconstruction from core-lacking encapsulin nanocompartments from Myxococcus xanthus | |||||||||
Sample |
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Keywords | Ferritin / encapsulin / HK97 fold / cryo electron microscopy / oxidative stress | |||||||||
Function / homology | : / Type 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 species | Myxococcus xanthus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | McHugh CA / Fontana J / Nemecek D / Cheng N / Aksyuk AA / Heymann JB / Winkler DC / Lam AS / Wall JS / Steven AC / Hoiczyk E | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5953.map.gz | 58.8 MB | EMDB map data format | |
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Header (meta data) | emd-5953-v30.xml emd-5953.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_5953_fsc.xml | 2.5 KB | Display | FSC data file |
Images | emd_5953.png | 79.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5953 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5953 | HTTPS FTP |
-Validation report
Summary document | emd_5953_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_5953_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_5953_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5953 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5953 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5953.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction from core-lacking encapsulin nanocompartments from Myxococcus xanthus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Core-lacking nanocompartments purified from Myxococcus xanthus
Entire | Name: Core-lacking nanocompartments purified from Myxococcus xanthus |
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Components |
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-Supramolecule #1000: Core-lacking nanocompartments purified from Myxococcus xanthus
Supramolecule | Name: 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
Macromolecule | Name: EncA / type: protein_or_peptide / ID: 1 / Name.synonym: Encapsulin nanocompartment, MXAN_3556 / Details: Major component, forms the shell. / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622 |
-Macromolecule #2: EncB
Macromolecule | Name: EncB / type: protein_or_peptide / ID: 2 / Name.synonym: Encapsulin nanocompartment, MXAN_3557 / Details: Located inside shell / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622 |
-Macromolecule #3: EncC
Macromolecule | Name: EncC / type: protein_or_peptide / ID: 3 / Name.synonym: Encapsulin nanocompartment, MXAN_4464 / Details: Located inside shell / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622 |
-Macromolecule #4: EncD
Macromolecule | Name: EncD / type: protein_or_peptide / ID: 4 / Name.synonym: Encapsulin nanocompartment, MXAN_2410 / Details: Located inside shell / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2 |
Grid | Details: 400 mesh carbon grid with thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 83 K / Instrument: LEICA KF80 |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Date | Aug 23, 2012 |
Image recording | Category: 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 beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder model: GATAN LIQUID NITROGEN |