Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans.
Journal, issue, pages	J Biol Chem, Vol. 299, Issue 1, Page 102784, Year 2023
Publish date	Dec 9, 2022
Authors	Domenica Farci / André T Graça / Luca Iesu / Daniele de Sanctis / Dario Piano /
PubMed 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.
External links	J Biol Chem / PubMed:36502921 / PubMed Central
Methods	EM (single particle)
Resolution	2.54 - 5.3 Å
Structure data	15382 8agd EMDB-15382: S-layer Deinoxanthin-Binding Complex, details of the stalk region PDB-8agd: Full SDBC and SOD assembly Method: EM (single particle) / Resolution: 3.5 Å EMDB-15384: S-layer Deinoxanthin-Binding Complex, details of the N-terminal end of the stalk region Method: EM (single particle) / Resolution: 5.3 Å EMDB-15487: SDBC and SOD assembly, composite map Method: EM (single particle) / Resolution: 3.5 Å PDB-8aca: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase Method: ELECTRON MICROSCOPY / Resolution: 2.54 Å PDB-8acq: S-layer Deinoxanthin-Binding Complex (SDBC), subunit DR_2577 assembled with its SOD DR_0644 Method: ELECTRON MICROSCOPY / Resolution: 2.54 Å
Chemicals	ChemComp-CU: COPPER (II) ION / Copper 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 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 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 ChemComp-FE: Unknown entry / Iron
Source	deinococcus radiodurans r1 (radioresistant)
Keywords	METAL BINDING PROTEIN / Superoxide Dismutase / S-layer Deinoxanthin-Binding Complex / Deinococcus radiodurans / Cell envelop / S-layer / STRUCTURAL PROTEIN / metal binding proteins / deinoxanthin / phosphoglycolipids / copper / iron