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- EMDB-15487: SDBC and SOD assembly, composite map -

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Basic information

Entry
Database: EMDB / ID: EMD-15487
TitleSDBC and SOD assembly, composite map
Map dataComposite map
Sample
  • Complex: SDBC and SOD assembly, composite map
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFarci D / Piano D
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science CentrePRO-2017/26/E/NZ1/00344 Poland
CitationJournal: J Biol Chem / Year: 2023
Title: The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans.
Authors: Domenica Farci / André T Graça / Luca Iesu / Daniele de Sanctis / Dario Piano /
Abstract: Deinococcus radiodurans is known for its remarkable ability to withstand harsh stressful conditions. The outermost layer of its cell envelope is a proteinaceous coat, the S-layer, essential for ...Deinococcus radiodurans is known for its remarkable ability to withstand harsh stressful conditions. The outermost layer of its cell envelope is a proteinaceous coat, the S-layer, essential for resistance to and interactions with the environment. The S-layer Deinoxanthin-binding complex (SDBC), one of the main units of the characteristic multilayered cell envelope of this bacterium, protects against environmental stressors and allows exchanges with the environment. So far, specific regions of this complex, the collar and the stalk, remained unassigned. Here, these regions are resolved by cryo-EM and locally refined. The resulting 3D map shows that the collar region of this multiprotein complex is a trimer of the protein DR_0644, a Cu-only superoxide dismutase (SOD) identified here to be efficient in quenching reactive oxygen species. The same data also showed that the stalk region consists of a coiled coil that extends into the cell envelope for ∼280 Å, reaching the inner membrane. Finally, the orientation and localization of the complex are defined by in situ cryo-electron crystallography. The structural organization of the SDBC couples fundamental UV antenna properties with the presence of a Cu-only SOD, showing here coexisting photoprotective and chemoprotective functions. These features suggests how the SDBC and similar protein complexes, might have played a primary role as evolutive templates for the origin of photoautotrophic processes by combining primary protective needs with more independent energetic strategies.
History
DepositionJul 29, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15487.png

Downloads & links

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Map

FileDownload / File: emd_15487.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Voxel sizeX=Y=Z: 0.818 Å
Density
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-0.4256629 - 0.75490254
Average (Standard dev.)-0.00034609254 (±0.007647016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-1-62
Dimensions642642703
Spacing642642703
CellA: 525.156 Å / B: 525.156 Å / C: 575.054 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SDBC and SOD assembly, composite map

EntireName: SDBC and SOD assembly, composite map
Components
  • Complex: SDBC and SOD assembly, composite map

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Supramolecule #1: SDBC and SOD assembly, composite map

SupramoleculeName: SDBC and SOD assembly, composite map / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Details: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. The map has to be used as a ...Details: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. The map has to be used as a consensus map of the full structure (PDB-8AGD).
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Molecular weightTheoretical: 800 KDa

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
Details: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. This map is a composite map of ...Details: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. The map has to be used as a consensus map of the full structure (PDB-8AGD).
Number images used: 252122

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