8PFH | pdb_00008pfh

Crystal structure of the yeast septin complex Shs1-Cdc12-Cdc3-Cdc10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 
    0.290 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.282 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 
    0.283 (Depositor) 

Starting Model: in silico
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Literature

The structure of a tetrameric septin complex reveals a hydrophobic element essential for NC-interface integrity.

Grupp, B.Denkhaus, L.Gerhardt, S.Vogele, M.Johnsson, N.Gronemeyer, T.

(2024) Commun Biol 7: 48-48

  • DOI: https://doi.org/10.1038/s42003-023-05734-w
  • Primary Citation Related Structures: 
    8PFH

  • PubMed Abstract: 

    The septins of the yeast Saccharomyces cerevisiae assemble into hetero-octameric rods by alternating interactions between neighboring G-domains or N- and C-termini, respectively. These rods polymerize end to end into apolar filaments, forming a ring beneath the prospective new bud that expands during the cell cycle into an hourglass structure. The hourglass finally splits during cytokinesis into a double ring. Understanding these transitions as well as the plasticity of the higher order assemblies requires a detailed knowledge of the underlying structures. Here we present the first X-ray crystal structure of a tetrameric Shs1-Cdc12-Cdc3-Cdc10 complex at a resolution of 3.2 Å. Close inspection of the NC-interfaces of this and other septin structures reveals a conserved contact motif that is essential for NC-interface integrity of yeast and human septins in vivo and in vitro. Using the tetrameric structure in combination with AlphaFold-Multimer allowed us to propose a model of the octameric septin rod.


  • Organizational Affiliation
    • Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany.

Macromolecule Content 

  • Total Structure Weight: 148.97 kDa 
  • Atom Count: 9,086 
  • Modeled Residue Count: 1,139 
  • Deposited Residue Count: 1,282 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CDC10 isoform 1300Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC10
UniProt
Find proteins for P25342 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25342 
Go to UniProtKB:  P25342
Entity Groups
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UniProt GroupP25342
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 3332Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC3YLR314CL8543.7
UniProt
Find proteins for P32457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32457 
Go to UniProtKB:  P32457
Entity Groups
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UniProt GroupP32457
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
CDC12 isoform 1330Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC12
UniProt
Find proteins for P32468 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32468 
Go to UniProtKB:  P32468
Entity Groups
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UniProt GroupP32468
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SHS1 isoform 1320Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SHS1
UniProt
Find proteins for Q07657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07657 
Go to UniProtKB:  Q07657
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07657
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free:  0.290 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.282 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 0.283 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 258.178α = 90
b = 69.373β = 109.68
c = 92.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references