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Yorodumi- EMDB-41078: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41078 | |||||||||
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Title | Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell | |||||||||
Map data | ||||||||||
Sample |
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Keywords | encapsulin / virus like particle / protein nanocompartment | |||||||||
Function / homology | : Function and homology information | |||||||||
Biological species | Acinetobacter baumannii 118362 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.78 Å | |||||||||
Authors | Andreas MP / Benisch R / Giessen TW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: A widespread bacterial protein compartment sequesters and stores elemental sulfur. Authors: Robert Benisch / Michael P Andreas / Tobias W Giessen / Abstract: Subcellular compartments often serve to store nutrients or sequester labile or toxic compounds. As bacteria mostly do not possess membrane-bound organelles, they often have to rely on protein-based ...Subcellular compartments often serve to store nutrients or sequester labile or toxic compounds. As bacteria mostly do not possess membrane-bound organelles, they often have to rely on protein-based compartments. Encapsulins are one of the most prevalent protein-based compartmentalization strategies found in prokaryotes. Here, we show that desulfurase encapsulins can sequester and store large amounts of crystalline elemental sulfur. We determine the 1.78-angstrom cryo-EM structure of a 24-nanometer desulfurase-loaded encapsulin. Elemental sulfur crystals can be formed inside the encapsulin shell in a desulfurase-dependent manner with l-cysteine as the sulfur donor. Sulfur accumulation can be influenced by the concentration and type of sulfur source in growth medium. The selectively permeable protein shell allows the storage of redox-labile elemental sulfur by excluding cellular reducing agents, while encapsulation substantially improves desulfurase activity and stability. These findings represent an example of a protein compartment able to accumulate and store elemental sulfur. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41078.map.gz | 204.2 MB | EMDB map data format | |
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Header (meta data) | emd-41078-v30.xml emd-41078.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41078_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_41078.png | 174.4 KB | ||
Filedesc metadata | emd-41078.cif.gz | 6.2 KB | ||
Others | emd_41078_half_map_1.map.gz emd_41078_half_map_2.map.gz | 198.3 MB 198.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41078 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41078 | HTTPS FTP |
-Validation report
Summary document | emd_41078_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41078_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41078_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_41078_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41078 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41078 | HTTPS FTP |
-Related structure data
Related structure data | 8t6rMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41078.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41078_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41078_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell
Entire | Name: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell |
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Components |
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-Supramolecule #1: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell
Supramolecule | Name: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Acinetinobacter baumannii 118362 family 2A encapsulin shell with internal cysteine desulfurase cargo protein |
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Source (natural) | Organism: Acinetobacter baumannii 118362 (bacteria) |
Molecular weight | Theoretical: 1.88 MDa |
-Macromolecule #1: Major membrane protein I
Macromolecule | Name: Major membrane protein I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii 118362 (bacteria) |
Molecular weight | Theoretical: 34.609195 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAKNTDKAQL ALGDHAARQL ANATKTAPQL STITPRWLTH LLQWIPVEAG IYRLNRVNNT DDIQVACTQR DEATLPQTFV DYAPEPREY FLNGVSTVLD VHTRVADLYS SPHDQIKEQL RLTIETIKER QESELINNPE YGLLASVTDD QRISTLNGPP T PDDLDDLL ...String: MAKNTDKAQL ALGDHAARQL ANATKTAPQL STITPRWLTH LLQWIPVEAG IYRLNRVNNT DDIQVACTQR DEATLPQTFV DYAPEPREY FLNGVSTVLD VHTRVADLYS SPHDQIKEQL RLTIETIKER QESELINNPE YGLLASVTDD QRISTLNGPP T PDDLDDLL RKVWKEPGFF LAHPDAIAAF GRECTRRGVP PPTVSLFGSQ FITWRGIPLI PSNKIPVEDG KTKILLLRVG EK RQGIVGL FQPGLAGEQS PGLSVRFMGI NRNAIASYLI SLYCSLAVLT DDALAVLDDV EVDKYHDYPV NYK UniProtKB: UNIPROTKB: A0A009HA42 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: 150 mM NaCl, 20 mM Tris pH 7.5 | |||||||||
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: 60 seconds at 5 mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: Blot force: 20 Blot time: 4 seconds Drain time: 0 Wait time: 0. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5936 / Average exposure time: 3.0 sec. / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 28.96 / Target criteria: cross-correlation coefficient |
Output model | PDB-8t6r: |