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- PDB-7zgy: S-layer Deinoxanthin Binding Complex, C3 symmetry -

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Basic information

Entry
Database: PDB / ID: 7zgy
TitleS-layer Deinoxanthin Binding Complex, C3 symmetry
ComponentsS-layer protein SlpA
KeywordsSTRUCTURAL PROTEIN / PROTEIN / S-layer / deinococcus radiodurans / DR_2577 / S-layer Deinoxanthin Binding Complex
Function / homology
Function and homology information


cell envelope / cell outer membrane
Similarity search - Function
: / S-layer protein SlpA, beta-barrel domain / : / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile.
Similarity search - Domain/homology
COPPER (II) ION / : / Chem-JPI / Chem-JPX / Chem-JQ6 / Outer membrane protein SlpA
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsFarci, D. / Piano, D.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentrePRO-2017/26/E/NZ1/00344 Poland
Polish National Science CentrePRO-2018/30/M/NZ1/00284 Poland
CitationJournal: 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
DepositionApr 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
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Revision 1.0Jul 13, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary / Category: em_admin / pdbx_entry_details
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Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,49724
Polymers371,5063
Non-polymers7,99121
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25930 Å2
ΔGint-280 kcal/mol
Surface area118680 Å2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein S-layer protein SlpA


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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Non-polymers , 5 types, 21 molecules

#2: 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
#3: 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
#4: 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
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE / FE (III) ION


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
Has protein modificationN

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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: S-layer Deinoxanthin Binding Complex, C3 Symmetry / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.8 MDa / Experimental value: YES
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 FIELD / 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
EM softwareName: PHENIX / Category: model 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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