8ONW | pdb_00008onw

Crystal structure of the hetero-dimeric complex from Archaeoglobus fulgidus PRC1 and PRC2 domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.240 (DCC) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division.

Nussbaum, P.Kureisaite-Ciziene, D.Bellini, D.van der Does, C.Kojic, M.Taib, N.Yeates, A.Tourte, M.Gribaldo, S.Loose, M.Lowe, J.Albers, S.V.

(2024) Nat Microbiol 9: 698-711

  • DOI: https://doi.org/10.1038/s41564-024-01600-5
  • Primary Citation of Related Structures:  
    8ONW, 8QZO

  • PubMed Abstract: 

    Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.


  • Organizational Affiliation
    • Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRC-barrel domain-containing proteinA,
C [auth B]
92Archaeoglobus fulgidusMutation(s): 0 
Gene Names: XD40_0572
UniProt
Find proteins for A0A117KMF0 (Archaeoglobus fulgidus)
Explore A0A117KMF0 
Go to UniProtKB:  A0A117KMF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A117KMF0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PRC-barrel domain-containing proteinB [auth H],
D [auth C],
F [auth E],
H [auth G]
76Archaeoglobus fulgidusMutation(s): 0 
Gene Names: XD40_0428
UniProt
Find proteins for A0A117KMK3 (Archaeoglobus fulgidus)
Explore A0A117KMK3 
Go to UniProtKB:  A0A117KMK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A117KMK3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PRC-barrel domain-containing proteinE [auth D],
G [auth F]
76Archaeoglobus fulgidusMutation(s): 0 
Gene Names: XD40_0572
UniProt
Find proteins for A0A117KMF0 (Archaeoglobus fulgidus)
Explore A0A117KMF0 
Go to UniProtKB:  A0A117KMF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A117KMF0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.240 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.086α = 90
b = 102.633β = 90
c = 112.323γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references, Structure summary