4AJ5

Crystal structure of the Ska core complex

• PDB DOI:  https://doi.org/10.2210/pdb4AJ5/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-02-15 Released: 2012-05-23 
• Deposition Author(s): Jeyaprakash, A.A., Santamaria, A., Jayachandran, U., Chan, Y.W., Benda, C., Nigg, E.A., Conti, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.280 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 

Literature

Structural and Functional Organization of the Ska Complex, a Key Component of the Kinetochore-Microtubule Interface.

Jeyaprakash, A.A., Santamaria, A., Jayachandran, U., Chan, Y.W., Benda, C., Nigg, E.A., Conti, E.

(2012) Mol Cell 46: 274

• PubMed: 22483620 
• DOI: https://doi.org/10.1016/j.molcel.2012.03.005
• Primary Citation of Related Structures:  
  4AJ5


• PubMed Abstract: 
  

The Ska complex is an essential mitotic component required for accurate cell division in human cells. It is composed of three subunits that function together to establish stable kinetochore-microtubule interactions in concert with the Ndc80 network. We show that the structure of the Ska core complex is a W-shaped dimer of coiled coils, formed by intertwined interactions between Ska1, Ska2, and Ska3. The C-terminal domains of Ska1 and Ska3 protrude at each end of the homodimer, bind microtubules in vitro when connected to the central core, and are essential in vivo. Mutations disrupting the central coiled coil or the dimerization interface result in chromosome congression failure followed by cell death. The Ska complex is thus endowed with bipartite and cooperative tubulin-binding properties at the ends of a 350 Å-long molecule. We discuss how this symmetric architecture might complement and stabilize the Ndc80-microtubule attachments with analogies to the yeast Dam1/DASH complex.

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Organizational Affiliation: 

Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Hetero 30-mer - A10B10C10 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 367.17 kDa 
• Atom Count: 21,691 
• Modelled Residue Count: 2,893 
• Deposited Residue Count: 3,150 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3	A [auth 1], AA [auth W], B [auth 2], BA [auth X], C [auth 3], CA [auth Y], D [auth 4], DA [auth Z], Y [auth U], Z [auth V]	101	Homo sapiens	Mutation(s): 1  Gene Names: SKA3, C13orf3, RAMA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IX90 (Homo sapiens) Explore Q8IX90  Go to UniProtKB:  Q8IX90
PHAROS:  Q8IX90

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1	E [auth A], F [auth B], G [auth C], H [auth D], I [auth E], J [auth F], K [auth G], L [auth H], M [auth I], N [auth J]	91	Homo sapiens	Mutation(s): 0  Gene Names: SKA1, C18orf24
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BD8 (Homo sapiens) Explore Q96BD8  Go to UniProtKB:  Q96BD8
PHAROS:  Q96BD8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2	O [auth K], P [auth L], Q [auth M], R [auth N], S [auth O], T [auth P], U [auth Q], V [auth R], W [auth S], X [auth T]	123	Homo sapiens	Mutation(s): 0  Gene Names: SKA2, FAM33A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVK7 (Homo sapiens) Explore Q8WVK7  Go to UniProtKB:  Q8WVK7
PHAROS:  Q8WVK7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.280 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.4	α = 90
b = 193.121	β = 95.21
c = 198.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Jeyaprakash, A.A., Santamaria, A., Jayachandran, U., Chan, Y.W., Benda, C., Nigg, E.A., Conti, E.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release