8SGD

Crystal Structure of CDC3(G) - CDC10(Delta 1-10) heterocomplex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


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Literature

A key piece of the puzzle: The central tetramer of the Saccharomyces cerevisiae septin protofilament and its implications for self-assembly.

Marques da Silva, R.Christe Dos Reis Saladino, G.Antonio Leonardo, D.D'Muniz Pereira, H.Andrea Sculaccio, S.Paula Ulian Araujo, A.Charles Garratt, R.

(2023) J Struct Biol 215: 107983-107983

  • DOI: https://doi.org/10.1016/j.jsb.2023.107983
  • Primary Citation of Related Structures:  
    8FWP, 8SGD

  • PubMed Abstract: 

    Septins, often described as the fourth component of the cytoskeleton, are structural proteins found in a vast variety of living beings. They are related to small GTPases and thus, generally, present GTPase activity which may play an important (although incompletely understood) role in their organization and function. Septins polymerize into long non-polar filaments, in which each subunit interacts with two others by alternating interfaces, NC and G. In Saccharomyces cerevisiae four septins are organized in the following manner, [Cdc11-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Cdc11] n in order to form filaments. Although septins were originally discovered in yeast and much is known regarding their biochemistry and function, only limited structural information about them is currently available. Here we present crystal structures of Cdc3/Cdc10 which provide the first view of the physiological interfaces formed by yeast septins. The G-interface has properties which place it in between that formed by SEPT2/SEPT6 and SEPT7/SEPT3 in human filaments. Switch I from Cdc10 contributes significantly to the interface, whereas in Cdc3 it is largely disorded. However, the significant negative charge density of the latter suggests it may have a unique role. At the NC-interface, we describe an elegant means by which the sidechain of a glutamine from helix α 0 imitates a peptide group in order to retain hydrogen-bond continuity at the kink between helices α 5 and α 6 in the neighbouring subunit, thereby justifying the conservation of the helical distortion. Its absence from Cdc11, along with this structure's other unusual features are critically discussed by comparison with Cdc3 and Cdc10.


  • Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CDC10 isoform 1
A, C
313Saccharomyces 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25342
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CDC3 isoform 1
B, D
309Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC3
UniProt
Find proteins for P32457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32457 
Go to UniProtKB:  P32457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32457
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
I [auth B],
U [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
N [auth C]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth B],
V [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
W [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.277α = 90
b = 154.271β = 90
c = 156.264γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2020/02897-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release