+Open data
-Basic information
Entry | Database: PDB / ID: 4pt2 | ||||||
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Title | Myxococcus xanthus encapsulin protein (EncA) | ||||||
Components | Encapsulin protein | ||||||
Keywords | VIRUS LIKE PARTICLE / HK97 fold / Shell protein | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Fontana, J. / Aksyuk, A.A. / Steven, A.C. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4pt2.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pt2.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pt2_validation.pdf.gz | 984.8 KB | Display | wwPDB validaton report |
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Full document | 4pt2_full_validation.pdf.gz | 1017.2 KB | Display | |
Data in XML | 4pt2_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 4pt2_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/4pt2 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/4pt2 | HTTPS FTP |
-Related structure data
Related structure data | 5917MC 5953C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 31691.977 Da / Num. of mol.: 3 / Fragment: UNP residues 8-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Gene: MXAN_3556 / Plasmid: pET12a-3556 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q1D6H4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Encapsulin protein (EncA) from Myxococcus xanthus / Type: COMPLEX |
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Buffer solution | Name: 10 mM Tris, 10 mM MgCl2 / pH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400 mesh carbon grid with thin carbon support |
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Temp: 83 K / Details: Plunged into liquid ethane (LEICA KF80) |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Dec 3, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 57620 X / Nominal defocus max: 1650 nm / Nominal defocus min: 600 nm |
Specimen holder | Specimen holder model: OTHER / Specimen holder type: Polara cartridge-loading system |
Image recording | Electron dose: 15 e/Å2 |
Image scans | Num. digital images: 157 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software | Name: Bsoft / Category: 3D reconstruction | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: Each micrograph | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: reference based / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14000 / Nominal pixel size: 1.102 Å / Actual pixel size: 1.102 Å Details: Final map was calculated dividing particles into two independent data sets Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 4.6→771.4 Å / SU ML: 1.04 / σ(F): 0 / Phase error: 43.52 / Stereochemistry target values: MLHL Details: Homology model of PDB entry 3DKT (I-TASSER), flexible fitting using MDFF and manual re-building using COOT, refined using structure factors derived from EMD-5917
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.6→771.4 Å
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Refine LS restraints |
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LS refinement shell |
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