3VZ9 | pdb_00003vz9

Crystal structure of the chicken Spc24-Spc25 globular domain

• PDB DOI: https://doi.org/10.2210/pdb3VZ9/pdb

• Classification: CELL CYCLE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-09 Released: 2013-04-03 
• Deposition Author(s): Nishino, T., Fukagawa, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.207 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

CENP-T provides a structural platform for outer kinetochore assembly

Nishino, T., Rago, F., Hori, T., Tomii, K., Cheeseman, I.M., Fukagawa, T.

(2013) EMBO J 32: 424-436

• PubMed: 23334297 
• DOI: https://doi.org/10.1038/emboj.2012.348
• Primary Citation Related Structures: 
  3VZ9, 3VZA


• PubMed Abstract: 
  

  The kinetochore forms a dynamic interface with microtubules from the mitotic spindle during mitosis. The Ndc80 complex acts as the key microtubule-binding complex at kinetochores. However, it is unclear how the Ndc80 complex associates with the inner kinetochore proteins that assemble upon centromeric chromatin. Here, based on a high-resolution structural analysis, we demonstrate that the N-terminal region of vertebrate CENP-T interacts with the 'RWD' domain in the Spc24/25 portion of the Ndc80 complex. Phosphorylation of CENP-T strengthens a cryptic hydrophobic interaction between CENP-T and Spc25 resulting in a phospho-regulated interaction that occurs without direct recognition of the phosphorylated residue. The Ndc80 complex interacts with both CENP-T and the Mis12 complex, but we find that these interactions are mutually exclusive, supporting a model in which two distinct pathways target the Ndc80 complex to kinetochores. Our results provide a model for how the multiple protein complexes at kinetochores associate in a phospho-regulated manner.

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Organizational Affiliation: 
• Department of Molecular Genetics, National Institute of Genetics and The Graduate University for Advanced Studies SOKENDAI, Shizuoka 411-8540, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 20.99 kDa 
• Atom Count: 1,617 
• Modeled Residue Count: 163 
• Deposited Residue Count: 179 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A [auth B]	106	Gallus gallus	Mutation(s): 0  Gene Names: SPC25

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spc24 protein	B [auth D]	73	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for R4GRT3 (Gallus gallus) Explore R4GRT3  Go to UniProtKB:  R4GRT3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.207 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.321	α = 90
b = 58.137	β = 90
c = 58.479	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Nishino, T., Fukagawa, T.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description