8V10

Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A communication hub for phosphoregulation of kinetochore-microtubule attachment.

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

(2024) Curr Biol 

  • DOI: https://doi.org/10.1016/j.cub.2024.04.067
  • Primary Citation of Related Structures:  
    8V10, 8V11

  • PubMed Abstract: 

    The Mps1 and Aurora B kinases regulate and monitor kinetochore attachment to spindle microtubules during cell division, ultimately ensuring accurate chromosome segregation. In yeast, the critical spindle attachment components are the Ndc80 and Dam1 complexes (Ndc80c and DASH/Dam1c, respectively). Ndc80c is a 600-Å-long heterotetramer that binds microtubules through a globular "head" at one end and centromere-proximal kinetochore components through a globular knob at the other end. Dam1c is a heterodecamer that forms a ring of 16-17 protomers around the shaft of the single kinetochore microtubule in point-centromere yeast. The ring coordinates the approximately eight Ndc80c rods per kinetochore. In published work, we showed that a site on the globular "head" of Ndc80c, including residues from both Ndc80 and Nuf2, binds a bipartite segment in the long C-terminal extension of Dam1. Results reported here show, both by in vitro binding experiments and by crystal structure determination, that the same site binds a conserved segment in the long N-terminal extension of Mps1. It also binds, less tightly, a conserved segment in the N-terminal extension of Ipl1 (yeast Aurora B). Together with results from experiments in yeast cells and from biochemical assays reported in two accompanying papers, the structures and graded affinities identify a communication hub for ensuring uniform bipolar attachment and for signaling anaphase onset.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein NDC80279Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NDC80HEC1TID3YIL144W
UniProt
Find proteins for P40460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P40460
Entity Groups  
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UniProt GroupP40460
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mps1/NUF2 chimera protein233Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MPS1RPK1YDL028CD2785NUF2YOL069W
EC: 2.7.12.2
UniProt
Find proteins for P54199 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P54199
Find proteins for P33895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P33895
Entity Groups  
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UniProt GroupsP33895P54199
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein SPC24100Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPC24YMR117CYM9718.16C
UniProt
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q04477
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UniProt GroupQ04477
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein SPC25115Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPC25YER018C
UniProt
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40014 
Go to UniProtKB:  P40014
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UniProt GroupP40014
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.657α = 90
b = 168.295β = 90
c = 230.214γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references