+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24816 | |||||||||
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Title | M. xanthus encapsulin EncA bound to EncB targeting peptide | |||||||||
Map data | M. xanthus EncA bound to EncB targeting peptide | |||||||||
Sample |
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Keywords | encapsulin / cargo protein / encapsulated ferritin / nanocage / 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 Function and homology information | |||||||||
Biological species | Myxococcus xanthus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Eren E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2022 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24816.map.gz | 66.7 MB | EMDB map data format | |
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Header (meta data) | emd-24816-v30.xml emd-24816.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24816_fsc.xml | 19.2 KB | Display | FSC data file |
Images | emd_24816.png | 237.5 KB | ||
Filedesc metadata | emd-24816.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24816 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24816 | HTTPS FTP |
-Validation report
Summary document | emd_24816_validation.pdf.gz | 769.6 KB | Display | EMDB validaton report |
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Full document | emd_24816_full_validation.pdf.gz | 769.2 KB | Display | |
Data in XML | emd_24816_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_24816_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24816 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24816 | HTTPS FTP |
-Related structure data
Related structure data | 7s2tMC 7s20C 7s21C 7s4qC 7s5cC 7s5kC 7s8tC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_24816.map.gz / Format: CCP4 / Size: 170.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | M. xanthus EncA bound to EncB targeting peptide | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 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 : EncA with T=1 symmetry
Entire | Name: EncA with T=1 symmetry |
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Components |
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-Supramolecule #1: EncA with T=1 symmetry
Supramolecule | Name: EncA with T=1 symmetry / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Myxococcus xanthus (bacteria) |
-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: Myxococcus xanthus (bacteria) |
Molecular weight | Theoretical: 33.505074 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: EncB targeting peptide
Macromolecule | Name: EncB targeting peptide / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Myxococcus xanthus (bacteria) |
Molecular weight | Theoretical: 1.354536 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ESHPLTVGSL RR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7s2t: |