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- EMDB-12169: S-layer Deinoxanthin Binding Complex (SDBC) -

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Basic information

Entry
Database: EMDB / ID: EMD-12169
TitleS-layer Deinoxanthin Binding Complex (SDBC)
Map data3D cryo-EM map of the S-layer Deinoxanthin Binding Complex (SDBC) isolated from the radio-resistant bacterium Deinococcus radiodurans
Sample
  • Complex: S-layer Deinoxanthin Binding Complex (SDBC)
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsFarci D / Kereiche S / Piano D
Funding support Poland, Czech Republic, 3 items
OrganizationGrant numberCountry
Polish National Science CentrePRO-2017/26/E/NZ1/00344 Poland
Polish National Science CentrePRO-2018/30/M/NZ1/00284 Poland
Grant Agency of the Czech Republic1825144Y Czech Republic
CitationJournal: J Biol Chem / Year: 2020
Title: Structural insights into the main S-layer unit of reveal a massive protein complex with porin-like features.
Authors: Domenica Farci / Mehmet Alphan Aksoyoglu / Stefano Francesco Farci / Jayesh Arun Bafna / Igor Bodrenko / Matteo Ceccarelli / Joanna Kirkpatrick / Mathias Winterhalter / Sami Kereïche / Dario Piano /
Abstract: In the extremophile bacterium , the outermost surface layer is tightly connected with the rest of the cell wall. This integrated organization provides a compact structure that shields the bacterium ...In the extremophile bacterium , the outermost surface layer is tightly connected with the rest of the cell wall. This integrated organization provides a compact structure that shields the bacterium against environmental stresses. The fundamental unit of this surface layer (S-layer) is the S-layer deinoxanthin-binding complex (SDBC), which binds the carotenoid deinoxanthin and provides both, thermostability and UV radiation resistance. However, the structural organization of the SDBC awaits elucidation. Here, we report the isolation of the SDBC with a gentle procedure consisting of lysozyme treatment and solubilization with the nonionic detergent -dodecyl-β-d-maltoside, which preserved both hydrophilic and hydrophobic components of the SDBC and allows the retention of several minor subunits. As observed by low-resolution single-particle analysis, we show that the complex possesses a porin-like structural organization, but is larger than other known porins. We also noted that the main SDBC component, the protein DR_2577, shares regions of similarity with known porins. Moreover, results from electrophysiological assays with membrane-reconstituted SDBC disclosed that it is a nonselective channel that has some peculiar gating properties, but also exhibits behavior typically observed in pore-forming proteins, such as porins and ionic transporters. The functional properties of this system and its porin-like organization provide information critical for understanding ion permeability through the outer cell surface of S-layer-carrying bacterial species.
History
DepositionJan 5, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateOct 27, 2021-
Current statusOct 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12169.png

Downloads & links

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Map

FileDownload / File: emd_12169.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D cryo-EM map of the S-layer Deinoxanthin Binding Complex (SDBC) isolated from the radio-resistant bacterium Deinococcus radiodurans
Voxel sizeX=Y=Z: 1.92 Å
Density
Contour LevelBy AUTHOR: 0.0191 / Movie #1: 0.025
Minimum - Maximum-0.04431046 - 0.092861205
Average (Standard dev.)0.0001492408 (±0.0053653135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.921.921.92
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z491.520491.520491.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0440.0930.000

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Supplemental data

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Sample components

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Entire : S-layer Deinoxanthin Binding Complex (SDBC)

EntireName: S-layer Deinoxanthin Binding Complex (SDBC)
Components
  • Complex: S-layer Deinoxanthin Binding Complex (SDBC)

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Supramolecule #1: S-layer Deinoxanthin Binding Complex (SDBC)

SupramoleculeName: S-layer Deinoxanthin Binding Complex (SDBC) / type: complex / ID: 1 / Parent: 0
Details: The SDBC is a hetero-oligomeric complex that constitutes the main protein complex of the S-layer of the radio-resistant bacterium Deinococcus radiodurans. This complex provides protection ...Details: The SDBC is a hetero-oligomeric complex that constitutes the main protein complex of the S-layer of the radio-resistant bacterium Deinococcus radiodurans. This complex provides protection against UV radiation and shows gating properties by allowing ions currents across the cell wall.
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Molecular weightExperimental: 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
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 2.7 µm / Calibrated defocus max: 3.3000000000000003 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 59000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number real images: 1573 / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11086
FSC plot (resolution estimation)

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