4CKM | pdb_00004ckm

Structure of the N-terminal domain of Leishmania SAS-6

• PDB DOI: https://doi.org/10.2210/pdb4CKM/pdb

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


• Deposited: 2014-01-07 Released: 2014-03-05 
• Deposition Author(s): van Breugel, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structure of the SAS-6 cartwheel hub from Leishmania major.

van Breugel, M., Wilcken, R., McLaughlin, S.H., Rutherford, T.J., Johnson, C.M.

(2014) Elife 3: e01812-e01812

• PubMed: 24596152 
• DOI: https://doi.org/10.7554/eLife.01812
• Primary Citation Related Structures: 
  4CKM, 4CKN, 4CKP


• PubMed Abstract: 
  

  Centrioles are cylindrical cell organelles with a ninefold symmetric peripheral microtubule array that is essential to template cilia and flagella. They are built around a central cartwheel assembly that is organized through homo-oligomerization of the centriolar protein SAS-6, but whether SAS-6 self-assembly can dictate cartwheel and thereby centriole symmetry is unclear. Here we show that Leishmania major SAS-6 crystallizes as a 9-fold symmetric cartwheel and provide the X-ray structure of this assembly at a resolution of 3.5 Å. We furthermore demonstrate that oligomerization of Leishmania SAS-6 can be inhibited by a small molecule in vitro and provide indications for its binding site. Our results firmly establish that SAS-6 can impose cartwheel symmetry on its own and indicate how this process might occur mechanistically in vivo. Importantly, our data also provide a proof-of-principle that inhibition of SAS-6 oligomerization by small molecules is feasible. DOI: http://dx.doi.org/10.7554/eLife.01812.001.

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Organizational Affiliation: 
• Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 59.18 kDa 
• Atom Count: 3,536 
• Modeled Residue Count: 425 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAS-6	A, B, C	180	Leishmania major	Mutation(s): 0
UniProt
Find proteins for E9AFQ5 (Leishmania major) Explore E9AFQ5  Go to UniProtKB:  E9AFQ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.25	α = 90
b = 84.25	β = 90
c = 239.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): van Breugel, M.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2014-03-19
  Changes: Database references
• Version 1.3: 2018-01-17
  Changes: Database references, Refinement description
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other