8G0Q | pdb_00008g0q

Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 
    0.285 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface.

Zahm, J.A.Jenni, S.Harrison, S.C.

(2023) Open Biol 13: 220378-220378

  • DOI: https://doi.org/10.1098/rsob.220378
  • Primary Citation of Related Structures:  
    8G0P, 8G0Q

  • PubMed Abstract: 

    The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 'loop' structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 'loop' is a stiff, α-helical 'switchback' structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore-microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.


  • Organizational Affiliation
    • Department of Biological Chemistry and Molecular Pharmacology, and.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein NDC80
A, C
287Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NDC80HEC1TID3YIL144W
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DASH complex subunit DAM1,Kinetochore protein NUF2
B, D
233Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DAM1YGR113WG6153NUF2YOL069W
UniProt
Find proteins for P33895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33895 
Go to UniProtKB:  P33895
Find proteins for P53267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53267 
Go to UniProtKB:  P53267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP53267P33895
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.997α = 90
b = 129.997β = 90
c = 216.308γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM124165
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection