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Open data
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Basic information
Entry | Database: PDB / ID: 7s5c | ||||||
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Title | M. xanthus ferritin-like protein EncB | ||||||
![]() | EncB | ||||||
![]() | CYTOSOLIC PROTEIN / encapsulin / cargo protein / encapsulated ferritin / ferroxidase | ||||||
Function / homology | : / EncFtn-like / encapsulin nanocompartment / Ferritin-like superfamily / intracellular iron ion homeostasis / metal ion binding / : / Encapsulin nanocompartment cargo protein EncB![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eren, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism. Authors: Elif Eren / Bing Wang / Dennis C Winkler / Norman R Watts / Alasdair C Steven / Paul T Wingfield / ![]() Abstract: Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical ...Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical applications. Encapsulin shell proteins are structurally similar to HK97 bacteriophage capsid protein and their function depends on the encapsulated cargos. The Myxococcus xanthus encapsulin system comprises EncA and three cargos: EncB, EncC, and EncD. EncB and EncC are similar to bacterial ferritins that can oxidize Fe to less toxic Fe. We analyzed EncA, EncB, and EncC by cryo-EM and X-ray crystallography. Cryo-EM shows that EncA cages can have T = 3 and T = 1 symmetry and that EncA T = 1 has a unique protomer arrangement. Also, we define EncB and EncC binding sites on EncA. X-ray crystallography of EncB and EncC reveals conformational changes at the ferroxidase center and additional metal binding sites, suggesting a mechanism for Fe oxidation and storage within the encapsulin shell. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.4 KB | Display | ![]() |
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PDB format | ![]() | 116.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 498.6 KB | Display | ![]() |
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Full document | ![]() | 503.7 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s20C ![]() 7s21C ![]() 7s2tC ![]() 7s4qC ![]() 7s5kC ![]() 7s8tC ![]() 5n5eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11986.373 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 20% PEG MME, 10% PEG 20000, 100 mM Tris-Bicine pH 8.5, 30 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→43.34 Å / Num. obs: 56065 / % possible obs: 95.4 % / Redundancy: 6.2 % / CC1/2: 1 / Rrim(I) all: 0.09 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4286 / CC1/2: 0.59 / Rrim(I) all: 0.87 / % possible all: 71.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N5E Resolution: 1.86→43.34 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.83 / Stereochemistry target values: ML
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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: 1.86→43.34 Å
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Refine LS restraints |
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LS refinement shell |
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