5TCS

Crystal structure of a Dwarf Ndc80 Tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Conserved Tetramer Junction in the Kinetochore Ndc80 Complex.

Valverde, R.Ingram, J.Harrison, S.C.

(2016) Cell Rep 17: 1915-1922

  • DOI: 10.1016/j.celrep.2016.10.065
  • Primary Citation of Related Structures:  
    5TCS, 5TD8

  • PubMed Abstract: 
  • The heterotetrameric Ndc80 complex establishes connectivity along the principal longitudinal axis of a kinetochore. Its two heterodimeric subcomplexes, each with a globular end and a coiled-coil shaft, connect end-to-end to create a ∼600 Å long rod spanning the gap from centromere-proximal structures to spindle microtubules ...

    The heterotetrameric Ndc80 complex establishes connectivity along the principal longitudinal axis of a kinetochore. Its two heterodimeric subcomplexes, each with a globular end and a coiled-coil shaft, connect end-to-end to create a ∼600 Å long rod spanning the gap from centromere-proximal structures to spindle microtubules. Neither subcomplex has a known function on its own, but the heterotetrameric organization and the characteristics of the junction are conserved from yeast to man. We have determined crystal structures of two shortened ("dwarf") Ndc80 complexes that contain the full tetramer junction and both globular ends. The junction connects two α-helical coiled coils through regions of four-chain and three-chain overlap. The complexity of its structure depends on interactions among conserved amino-acid residues, suggesting a binding site for additional cellular factor(s) not yet identified.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Howard Hughes Medical Institute, 250 Longwood Avenue, Boston, MA 02115, USA. Electronic address: harrison@crystal.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore protein NDC80A277Saccharomyces cerevisiae S288CMutation(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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore protein NUF2B215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUF2YOL069W
UniProt
Find proteins for P33895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33895 
Go to UniProtKB:  P33895
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UniProt GroupP33895
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore protein SPC24C100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC24YMR117CYM9718.16C
UniProt
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04477 
Go to UniProtKB:  Q04477
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UniProt GroupQ04477
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore protein SPC25D115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC25YER018C
UniProt
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40014 
Go to UniProtKB:  P40014
Entity Groups  
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UniProt GroupP40014
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.381α = 90
b = 186.593β = 90
c = 122.039γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing

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: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-11-30
    Changes: Database references
  • Version 1.2: 2017-08-09
    Changes: Database references
  • Version 2.0: 2019-11-20
    Changes: Atomic model, Author supporting evidence