5JO8 | pdb_00005jo8

CEP104 TOG domain

• PDB DOI: https://doi.org/10.2210/pdb5JO8/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-02 Released: 2016-07-20 
• Deposition Author(s): Rezabkova, L., Kraatz, S.H.W.
• Funding Organization(s): Marie Curie IEF, European Molecular Biology Organization

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Biophysical and Structural Characterization of the Centriolar Protein Cep104 Interaction Network.

Rezabkova, L., Kraatz, S.H., Akhmanova, A., Steinmetz, M.O., Kammerer, R.A.

(2016) J Biological Chem 291: 18496-18504

• PubMed: 27402853 
• DOI: https://doi.org/10.1074/jbc.M116.739771
• Primary Citation Related Structures: 
  5JO8


• PubMed Abstract: 
  

  Dysfunction of cilia is associated with common genetic disorders termed ciliopathies. Knowledge on the interaction networks of ciliary proteins is therefore key for understanding the processes that are underlying these severe diseases and the mechanisms of ciliogenesis in general. Cep104 has recently been identified as a key player in the regulation of cilia formation. Using a combination of sequence analysis, biophysics, and x-ray crystallography, we obtained new insights into the domain architecture and interaction network of the Cep104 protein. We solved the crystal structure of the tumor overexpressed gene (TOG) domain, identified Cep104 as a novel tubulin-binding protein, and biophysically characterized the interaction of Cep104 with CP110, Cep97, end-binding (EB) protein, and tubulin. Our results represent a solid platform for the further investigation of the microtubule-EB-Cep104-tubulin-CP110-Cep97 network of proteins. Ultimately, such studies should be of importance for understanding the process of cilia formation and the mechanisms underlying different ciliopathies.

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Organizational Affiliation: 
• From the Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland and.
Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
From the Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland and [e-mail].

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: 31.38 kDa 
• Atom Count: 2,321 
• Modeled Residue Count: 256 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CEP104	A	279	Gallus gallus	Mutation(s): 0  Gene Names: CEP104

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.36	α = 90
b = 57.22	β = 90
c = 102.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Rezabkova, L., Kraatz, S.H.W.

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Funding Organization	Location	Grant Number
Marie Curie IEF	Belgium	--
European Molecular Biology Organization	Germany	--

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-09-07
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references