8G0P

Crystal structure of the human Ndc80:Nuf2 loop region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 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 homolog143Homo sapiensMutation(s): 0 
Gene Names: NDC80HECHEC1KNTC2
UniProt & NIH Common Fund Data Resources
Find proteins for O14777 (Homo sapiens)
Explore O14777 
Go to UniProtKB:  O14777
GTEx:  ENSG00000080986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14777
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein Nuf298Homo sapiensMutation(s): 0 
Gene Names: NUF2CDCA1NUF2R
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZD4 (Homo sapiens)
Explore Q9BZD4 
Go to UniProtKB:  Q9BZD4
GTEx:  ENSG00000143228 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZD4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.903α = 90
b = 72.259β = 98.56
c = 80.065γ = 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
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