8AGD

Full SDBC and SOD assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans.

Farci, D.Graca, A.T.Iesu, L.de Sanctis, D.Piano, D.

(2023) J Biol Chem 299: 102784-102784

  • DOI: https://doi.org/10.1016/j.jbc.2022.102784
  • Primary Citation of Related Structures:  
    8ACA, 8ACQ, 8AGD

  • 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 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.


  • Organizational Affiliation

    Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Chemistry, Umeå University, Umeå, Sweden; Department of Life and Environmental Sciences, Laboratory of Plant Physiology and Photobiology, University of Cagliari, Cagliari, Italy. Electronic address: domenica.farci@unica.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-layer protein SlpA
A, B, C
1,167Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9RRB6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RRB6 
Go to UniProtKB:  Q9RRB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RRB6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide Dismutase (only-Cu)D [auth H],
E [auth I],
F [auth L]
206Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9RWM2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RWM2 
Go to UniProtKB:  Q9RWM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RWM2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JPX (Subject of Investigation/LOI)
Query on JPX

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
P [auth B]
[(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
C48 H91 N2 O15 P
BORXCJRMZBMSCX-GUINJWSRSA-N
JQ6 (Subject of Investigation/LOI)
Query on JQ6

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth B],
W [auth C]
[(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
C39 H73 N2 O15 P
ZPGLDLNPYVCZJR-XTLGHBECSA-N
JPI (Subject of Investigation/LOI)
Query on JPI

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B],
V [auth C]
(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
C40 H80 O3
HMWJPEUVPLHAER-VMKFVPKQSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
BA [auth H]
CA [auth I]
DA [auth L]
J [auth A]
K [auth A]
BA [auth H],
CA [auth I],
DA [auth L],
J [auth A],
K [auth A],
L [auth A],
R [auth B],
S [auth B],
T [auth B],
X [auth C],
Y [auth C],
Z [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AA [auth C],
M [auth A],
U [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandPRO-2017/26/E/NZ1/00344

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection