2Y3V | pdb_00002y3v

N-terminal head domain of Danio rerio SAS-6

• PDB DOI: https://doi.org/10.2210/pdb2Y3V/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-27 Released: 2011-02-09 
• Deposition Author(s): van Breugel, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Structures of SAS-6 suggest its organization in centrioles.

van Breugel, M., Hirono, M., Andreeva, A., Yanagisawa, H.A., Yamaguchi, S., Nakazawa, Y., Morgner, N., Petrovich, M., Ebong, I.O., Robinson, C.V., Johnson, C.M., Veprintsev, D., Zuber, B.

(2011) Science 331: 1196-1199

• PubMed: 21273447 
• DOI: https://doi.org/10.1126/science.1199325
• Primary Citation Related Structures: 
  2Y3V, 2Y3W


• PubMed Abstract: 
  

  Centrioles are cylindrical, ninefold symmetrical structures with peripheral triplet microtubules strictly required to template cilia and flagella. The highly conserved protein SAS-6 constitutes the center of the cartwheel assembly that scaffolds centrioles early in their biogenesis. We determined the x-ray structure of the amino-terminal domain of SAS-6 from zebrafish, and we show that recombinant SAS-6 self-associates in vitro into assemblies that resemble cartwheel centers. Point mutations are consistent with the notion that centriole formation in vivo depends on the interactions that define the self-assemblies observed here. Thus, these interactions are probably essential to the structural organization of cartwheel centers.

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Organizational Affiliation: 
• Medical Research Council-Laboratory of Molecular Biology (MRC-LMB), Hills Road, Cambridge, UK. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.1 kDa 
• Atom Count: 5,430 
• Modeled Residue Count: 617 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG	A, B, C, D	159	Danio rerio	Mutation(s): 0
UniProt
Find proteins for Q7ZVT3 (Danio rerio) Explore Q7ZVT3  Go to UniProtKB:  Q7ZVT3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.99	α = 90
b = 95.27	β = 90
c = 129.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): van Breugel, M.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Database references
• Version 1.4: 2024-05-01
  Changes: Data collection, Database references, Other, Refinement description