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- PDB-8aca: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 8aca
TitleSDBC DR_0644 subunit, only-Cu Superoxide Dismutase
ComponentsDR_0644, only-Cu Superoxide Dismutase
KeywordsMETAL BINDING PROTEIN / Superoxide Dismutase / S-layer Deinoxanthin-Binding Complex / Deinococcus radiodurans / Cell envelop / S-layer
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / COPPER (II) ION / CHRD domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsFarci, D. / Piano, D.
Funding support Poland, 1items
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 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DR_0644, only-Cu Superoxide Dismutase
B: DR_0644, only-Cu Superoxide Dismutase
C: DR_0644, only-Cu Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8576
Polymers62,6673
Non-polymers1913
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5210 Å2
ΔGint-24 kcal/mol
Surface area18710 Å2
MethodPISA

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Components

#1: Protein DR_0644, only-Cu Superoxide Dismutase


Mass: 20888.949 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RWM2
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1.3 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252122 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422104
ELECTRON MICROSCOPYf_angle_d0.730012
ELECTRON MICROSCOPYf_dihedral_angle_d12.1827908
ELECTRON MICROSCOPYf_chiral_restr0.0493228
ELECTRON MICROSCOPYf_plane_restr0.0034032

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