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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24814 | |||||||||
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Title | M. xanthus encapsulin shell protein EncA with T=3 symmetry | |||||||||
![]() | EncA with T=3 symmetry | |||||||||
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![]() | nanocage / encapsulin / iron storage / bacterial nano-compartment / CYTOSOLIC PROTEIN / VIRUS LIKE PARTICLE | |||||||||
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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 52.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.1 KB | Display | ![]() |
Images | ![]() | 250.7 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 700.1 KB | Display | ![]() |
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Full document | ![]() | 699.6 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s20MC ![]() 7s21C ![]() 7s2tC ![]() 7s4qC ![]() 7s5cC ![]() 7s5kC ![]() 7s8tC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | EncA with T=3 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : EncA with T=3 symmetry
Entire | Name: EncA with T=3 symmetry |
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Components |
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-Supramolecule #1: EncA with T=3 symmetry
Supramolecule | Name: EncA with T=3 symmetry / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: EncA
Macromolecule | Name: EncA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.505074 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHMPL EPHFMPDFLG HAENPLREEE WARLNETVIQ VARRSLVGRR ILDIYGPLGA GVQTVPYDEF QGVSPGAVDI VGEQETAMV FTDARKFKTI PIIYKDFLLH WRDIEAARTH NMPLDVSAAA GAAALCAQQE DELIFYGDAR LGYEGLMTAN G RLTVPLGD ...String: MHHHHHHMPL EPHFMPDFLG HAENPLREEE WARLNETVIQ VARRSLVGRR ILDIYGPLGA GVQTVPYDEF QGVSPGAVDI VGEQETAMV FTDARKFKTI PIIYKDFLLH WRDIEAARTH NMPLDVSAAA GAAALCAQQE DELIFYGDAR LGYEGLMTAN G RLTVPLGD WTSPGGGFQA IVEATRKLNE QGHFGPYAVV LSPRLYSQLH RIYEKTGVLE IETIRQLASD GVYQSNRLRG ES GVVVSTG RENMDLAVSM DMVAAYLGAS RMNHPFRVLE ALLLRIKHPD AICTLEGAGA TERR UniProtKB: Type 1 encapsulin shell protein EncA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.3 / Details: 20 mM HEPES, pH 7.3, 150 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7s20: |