7KDF

Structure of Stu2 Bound to dwarf Ndc80c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of Stu2 recruitment to yeast kinetochores.

Zahm, J.A.Stewart, M.G.Carrier, J.S.Harrison, S.C.Miller, M.P.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.65389
  • Primary Citation of Related Structures:  
    7KDF

  • PubMed Abstract: 

    Chromosome segregation during cell division requires engagement of kinetochores of sister chromatids with microtubules emanating from opposite poles. As the corresponding microtubules shorten, these 'bioriented' sister kinetochores experience tension-dependent stabilization of microtubule attachments. The yeast XMAP215 family member and microtubule polymerase, Stu2, associates with kinetochores and contributes to tension-dependent stabilization in vitro. We show here that a C-terminal segment of Stu2 binds the four-way junction of the Ndc80 complex (Ndc80c) and that residues conserved both in yeast Stu2 orthologs and in their metazoan counterparts make specific contacts with Ndc80 and Spc24. Mutations that perturb this interaction prevent association of Stu2 with kinetochores, impair cell viability, produce biorientation defects, and delay cell cycle progression. Ectopic tethering of the mutant Stu2 species to the Ndc80c junction restores wild-type function in vivo. These findings show that the role of Stu2 in tension-sensing depends on its association with kinetochores by binding with Ndc80c.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Howard Hughes Medical Institute, Boston, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NDC80 isoform 1,NDC80 isoform 1277Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NDC80GI526_G0001489
UniProt
Find proteins for P40460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40460 
Go to UniProtKB:  P40460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40460
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NUF2 isoform 1,NUF2 isoform 1215Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUF2GI526_G0005257
UniProt
Find proteins for P33895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33895 
Go to UniProtKB:  P33895
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33895
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spc24100Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04477 
Go to UniProtKB:  Q04477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04477
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SPC25 isoform 1,SPC25 isoform 1115Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPC25GI526_G0001792
UniProt
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40014 
Go to UniProtKB:  P40014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40014
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
STU233Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P46675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46675 
Go to UniProtKB:  P46675
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46675
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.886α = 90
b = 183.175β = 90
c = 124.317γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection