3SQI

DNA binding domain of Ndc10

• PDB DOI:  https://doi.org/10.2210/pdb3SQI/pdb
• NAKB: 3SQI

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Kluyveromyces lactis NRRL Y-1140
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-05 Released: 2011-12-07 
• Deposition Author(s): Cho, U.S., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.251 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

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

• PubMed: 22139014 
• 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.68 kDa 
• Atom Count: 3,811 
• Modelled Residue Count: 418 
• Deposited Residue Count: 564 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KLLA0E03807p	A	534	Kluyveromyces lactis NRRL Y-1140	Mutation(s): 0  Gene Names: KLLA0E03807g, KLLA0_E03807g
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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')	B	15	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)-3')	C	15	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.251 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.303	α = 90
b = 147.536	β = 90
c = 95.639	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Cho, U.S., Harrison, S.C.

Revision History  

• 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