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- EMDB-15382: S-layer Deinoxanthin-Binding Complex, details of the stalk region -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-15382
TitleS-layer Deinoxanthin-Binding Complex, details of the stalk region
Map datamap
Sample
  • Complex: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane / lipid binding
Similarity search - Function
: / S-layer protein SlpA, beta-barrel / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Outer membrane protein SlpA / CHRD domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFarci D / Graca AT / 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 12, 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_15382.png

Downloads & links

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Map

FileDownload / File: emd_15382.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 640 pix.
= 523.52 Å		0.82 Å/pix.
x 640 pix.
= 523.52 Å		0.82 Å/pix.
x 640 pix.
= 523.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.818 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.17249326 - 0.32153538
Average (Standard dev.)-0.00040493358 (±0.007565224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 523.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_15382_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_15382_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SDBC DR_0644 subunit, only-Cu Superoxide Dismutase

EntireName: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase
Components
  • Complex: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase

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Supramolecule #1: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase

SupramoleculeName: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)

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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 / Number images used: 252122
FSC plot (resolution estimation)

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