3SQI | pdb_00003sqi

DNA binding domain of Ndc10

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Ndc10 is a platform for inner kinetochore assembly in budding yeast.

Cho, U.S., Harrison, S.C.

(2011) Nat Struct Mol Biol 19: 48-55

  • DOI: https://doi.org/10.1038/nsmb.2178
  • Primary Citation of Related Structures:  
    3SQI, 3T79

  • PubMed Abstract: 

    Kinetochores link centromeric DNA to spindle microtubules and ensure faithful chromosome segregation during mitosis. In point-centromere yeasts, the CBF3 complex Skp1-Ctf13-(Cep3)(2)-(Ndc10)(2) recognizes a conserved centromeric DNA element through contacts made by Cep3 and Ndc10. We describe here the five-domain organization of Kluyveromyces lactis Ndc10 and the structure at 2.8 Å resolution of domains I-II (residues 1-402) bound to DNA. The structure resembles tyrosine DNA recombinases, although it lacks both endonuclease and ligase activities. Structural and biochemical data demonstrate that each subunit of the Ndc10 dimer binds a separate fragment of DNA, suggesting that Ndc10 stabilizes a DNA loop at the centromere. We describe in vitro association experiments showing that specific domains of Ndc10 interact with each of the known inner-kinetochore proteins or protein complexes in budding yeast. We propose that Ndc10 provides a central platform for inner-kinetochore assembly.

    • Organizational Affiliation: 
    • Jack and Eileen Connors Structural Biology Laboratory and Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0E03807p534Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0E03807g
UniProt
Find proteins for Q6CPM4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CPM4 
Go to UniProtKB:  Q6CPM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CPM4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')15N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)-3')15N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.303α = 90
b = 147.536β = 90
c = 95.639γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references
  • Version 1.2: 2012-01-18
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references