+Open data
-Basic information
Entry | Database: PDB / ID: 7zgx | |||||||||
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Title | S-layer Deinoxanthin Binding Complex, C1 symmetry | |||||||||
Components | S-layer protein SlpA | |||||||||
Keywords | STRUCTURAL PROTEIN / PROTEIN / S-layer / deinococcus radiodurans / DR_2577 / S-layer Deinoxanthin Binding Complex | |||||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transport / cell outer membrane / lipid binding Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Farci, D. / Piano, D. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: J Biol Chem / Year: 2022 Title: The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions. Authors: Domenica Farci / Patrycja Haniewicz / Daniele de Sanctis / Luca Iesu / Sami Kereïche / Mathias Winterhalter / Dario Piano / Abstract: The radiation-resistant bacterium Deinococcus radiodurans is known as the world's toughest bacterium. The S-layer of D. radiodurans, consisting of several proteins on the surface of the cellular ...The radiation-resistant bacterium Deinococcus radiodurans is known as the world's toughest bacterium. The S-layer of D. radiodurans, consisting of several proteins on the surface of the cellular envelope and intimately associated with the outer membrane, has therefore been useful as a model for structural and functional studies. Its main proteinaceous unit, the S-layer deinoxanthin-binding complex (SDBC), is a hetero-oligomeric assembly known to contribute to the resistance against environmental stress and have porin functional features; however, its precise structure is unknown. Here, we resolved the structure of the SDBC at ∼2.5 Å resolution by cryo-EM and assigned the sequence of its main subunit, the protein DR_2577. This structure is characterized by a pore region, a massive β-barrel organization, a stalk region consisting of a trimeric coiled coil, and a collar region at the base of the stalk. We show that each monomer binds three Cu ions and one Fe ion and retains one deinoxanthin molecule and two phosphoglycolipids, all exclusive to D. radiodurans. Finally, electrophysiological characterization of the SDBC shows that it exhibits transport properties with several amino acids. Taken together, these results highlight the SDBC as a robust structure displaying both protection and sieving functions that facilitates exchanges with the environment. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zgx.cif.gz | 480.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zgx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zgx_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7zgx_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7zgx_validation.xml.gz | 95.3 KB | Display | |
Data in CIF | 7zgx_validation.cif.gz | 140.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/7zgx ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zgx | HTTPS FTP |
-Related structure data
Related structure data | 14714MC 7zgyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 123835.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans R1 (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 References: UniProt: Q9RRB6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex C1 symmetry / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.8 MDa / Experimental value: YES |
Source (natural) | Organism: Deinococcus radiodurans R1 (radioresistant) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1.3 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252122 / Symmetry type: POINT | ||||||||||||||||||||||||
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