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- PDB-8agd: Full SDBC and SOD assembly -

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Basic information

Entry
Database: PDB / ID: 8agd
TitleFull SDBC and SOD assembly
Components
  • S-layer protein SlpA
  • Superoxide Dismutase (only-Cu)
KeywordsSTRUCTURAL PROTEIN / S-layer Deinoxanthin-Binding Complex / Superoxide Dismutase / Deinococcus radiodurans / Cell envelop / S-layer / Metal binding protein
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
COPPER (II) ION / : / Chem-JPI / Chem-JPX / Chem-JQ6 / Outer membrane protein SlpA / CHRD domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFarci, D. / Graca, A.T. / 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 19, 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

Downloads & links

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Assembly

Deposited unit
A: S-layer protein SlpA
B: S-layer protein SlpA
C: S-layer protein SlpA
H: Superoxide Dismutase (only-Cu)
I: Superoxide Dismutase (only-Cu)
L: Superoxide Dismutase (only-Cu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,35530
Polymers434,1736
Non-polymers8,18224
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43110 Å2
ΔGint-376 kcal/mol
Surface area164270 Å2
MethodPISA

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Components

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Protein , 2 types, 6 molecules ABCHIL

#1: Protein S-layer protein SlpA / / DR_2577


Mass: 123835.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RRB6
#2: Protein Superoxide Dismutase (only-Cu) / SOD / DR_2577


Mass: 20888.949 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RWM2

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Non-polymers , 5 types, 24 molecules

#3: Chemical ChemComp-JPI / (3~{S},5~{R},6~{R})-5-[(3~{S},7~{R},12~{S},16~{S},20~{S})-3,7,12,16,20,24-hexamethyl-24-oxidanyl-pentacosyl]-4,4,6-trimethyl-cyclohexane-1,3-diol


Mass: 609.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H80O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-JQ6 / [(2~{S})-2-acetyloxy-3-[[(2~{S})-3-[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-3-(octadecanoylamino)-4,5-bis(oxidanyl)oxan-2-yl]oxy-1-oxidanylidene-1-(pentylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propyl] ethanoate


Mass: 840.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H73N2O15P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-JPX / [(2~{S})-3-[[(2~{S})-3-[(2~{S},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(propanoylamino)oxan-2-yl]oxy-1-oxidanylidene-1-(pentadecylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-2-octanoyloxy-propyl] decanoate


Mass: 967.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C48H91N2O15P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

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: Full SDBC and SOD assembly / Type: COMPLEX
Details: The pdb is based on the maps with identifiers EMDB-14715, EMD-15382, and EMD-15384.
Entity ID: #2 / 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
VitrificationCryogen 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252122
Details: The pdb is based on the maps with identifiers EMD-15382 (3.5 A resolution), EMDB-14715 (2.54 A resolution), and EMD-15384 (5.3 A resolution).
Symmetry type: POINT

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