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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell | |||||||||
![]() | Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Andreas MP / Jones JA / Giessen TW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae. Authors: Jesse A Jones / Michael P Andreas / Tobias W Giessen / ![]() Abstract: Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress ...Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen Klebsiella pneumoniae. By combining cryo-electron microscopy with TP and TP-binding site mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 204.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.6 KB | Display | ![]() |
Images | ![]() | 158.8 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 200.5 MB 200.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u50MC ![]() 8u4zC ![]() 8u51C M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_41905_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
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Density Histograms |
-Half map: Half Map 2
File | emd_41905_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell
Entire | Name: Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell |
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Components |
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-Supramolecule #1: Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell
Supramolecule | Name: Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: Klebsiella pneumoniae family 1 encapsulin shell
Supramolecule | Name: Klebsiella pneumoniae family 1 encapsulin shell / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Klebsiella pneumoniae encapsulated DyP peroxidase
Supramolecule | Name: Klebsiella pneumoniae encapsulated DyP peroxidase / type: complex / ID: 3 / Parent: 2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Klebsiella pneumoniae family 1 encapsulin shell
Macromolecule | Name: Klebsiella pneumoniae family 1 encapsulin shell / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 28.841129 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MNNLHRELAP VSDAAWEQIE EEASRTLKRF LAARRVVDVS DPQGPAFSAV GTGHVTRLEG PGDSVGAVKR QSQPVVEFRV PFILTRQAI DDVERGSQDS DWSPLKEAAR KIAGAEDRAV FDGYAAAGIG GIRPQSSNSP LTLPVAASGY PDVIARALDQ L RVAGVNGP ...String: MNNLHRELAP VSDAAWEQIE EEASRTLKRF LAARRVVDVS DPQGPAFSAV GTGHVTRLEG PGDSVGAVKR QSQPVVEFRV PFILTRQAI DDVERGSQDS DWSPLKEAAR KIAGAEDRAV FDGYAAAGIG GIRPQSSNSP LTLPVAASGY PDVIARALDQ L RVAGVNGP YHLVLGENAY TLITSGNEDG YPVLQHIHRL IDGEIVWAPA IEGGVLLSTR GGDFAMDIGQ DISIGYLSHT AT HVELYLQ ESFTFRTLTS EAVVSLLPSE D |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 3.0 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM Tris pH 7.5, 150 mM NaCl | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharged for 60 seconds at 5 mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force: 20 Blot time: 4 seconds. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 1183 / Average exposure time: 5.0 sec. / Average electron dose: 41.67 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refinement using Phenix v1.20.1-4487-000. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 95.2 / Target criteria: Cross-correlation coefficient |
Output model | ![]() PDB-8u50: |