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- EMDB-43290: Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loa... -
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Open data
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Basic information
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Title | Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo | |||||||||
![]() | EncA-EncD encapsulin cryo-EM map | |||||||||
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Function / homology | Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Eren E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity. Authors: Elif Eren / Norman R Watts / James F Conway / Paul T Wingfield / ![]() Abstract: Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic ...Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe to Fe for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 73.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 22.5 KB | Display | ![]() |
Images | ![]() | 255.8 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 471.3 MB 470.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vjoMC ![]() 8vjnC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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-EncD encapsulin cryo-EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: EncA-EncD halfmap1
File | emd_43290_half_map_1.map | ||||||||||||
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Annotation | EncA-EncD halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EncA-EncD halfmap2
File | emd_43290_half_map_2.map | ||||||||||||
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Annotation | EncA-EncD halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Icosahedral encapsulin EncA particles in complex with cargo prote...
Entire | Name: Icosahedral encapsulin EncA particles in complex with cargo protein EncD |
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Components |
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-Supramolecule #1: Icosahedral encapsulin EncA particles in complex with cargo prote...
Supramolecule | Name: Icosahedral encapsulin EncA particles in complex with cargo protein EncD 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 |
-Macromolecule #2: Encapsulin nanocompartment cargo protein EncD
Macromolecule | Name: Encapsulin nanocompartment cargo protein EncD / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 859.992 Da |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GLTVGSLRG UniProtKB: Encapsulin nanocompartment cargo protein EncD |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.3 / Details: 20mM HEPES, 150mM NaCl |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |