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- EMDB-41078: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell -

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Basic information

Entry
Database: EMDB / ID: EMD-41078
TitleAcinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell
Map data
Sample
  • Complex: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell
    • Protein or peptide: Major membrane protein I
Keywordsencapsulin / virus like particle / protein nanocompartment
Function / homology:
Function and homology information
Biological speciesAcinetobacter baumannii 118362 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.78 Å
AuthorsAndreas MP / Benisch R / Giessen TW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM133325-04 United States
CitationJournal: 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
DepositionJun 17, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41078.png

Downloads & links

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Map

FileDownload / File: emd_41078.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-1.3587108 - 2.7459903
Average (Standard dev.)0.016047109 (±0.1295656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41078_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41078_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell

EntireName: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell
Components
  • Complex: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell
    • Protein or peptide: Major membrane protein I

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Supramolecule #1: Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell

SupramoleculeName: 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
Source (natural)Organism: Acinetobacter baumannii 118362 (bacteria)
Molecular weightTheoretical: 1.88 MDa

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Macromolecule #1: Major membrane protein I

MacromoleculeName: Major membrane protein I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii 118362 (bacteria)
Molecular weightTheoretical: 34.609195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMC4H11NO3tris(hydroxymethyl)aminomethane

Details: 150 mM NaCl, 20 mM Tris pH 7.5
GridModel: 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
VitrificationCryogen 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.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 695842
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab-initio model with I symmetry
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 1.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 596718
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6x8m


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 28.96 / Target criteria: cross-correlation coefficient
Output model

PDB-8t6r:
Acinetobacter baumannii 118362 family 2A cargo-loaded encapsulin shell

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