Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.79 kDa 
• Atom Count: 8626 
• Modelled Residue Count: 1091 
• Deposited Residue Count: 1152 
• Unique protein chains: 4

4F6R

Tubulin:Stathmin-like domain complex

• PDB DOI: 10.2210/pdb4F6R/pdb

• Classification: CELL CYCLE
• Organism(s): Ovis aries, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-15 Released: 2012-07-18 
• Deposition Author(s): Gigant, B., Mignot, I., Knossow, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.201 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Design and characterization of modular scaffolds for tubulin assembly.

Mignot, I., Pecqueur, L., Dorleans, A., Karuppasamy, M., Ravelli, R.B., Dreier, B., Pluckthun, A., Knossow, M., Gigant, B.

(2012) J Biol Chem 287: 31085-31094

• PubMed: 22791712 
• DOI: 10.1074/jbc.M112.383869
• Primary Citation of Related Structures:  
  4F61, 4F6R


• PubMed Abstract: 
  

In cells, microtubule dynamics is regulated by stabilizing and destabilizing factors. Whereas proteins in both categories have been identified, their mechanism of action is rarely understood at the molecular level. This is due in part to the difficulties faced in structural approaches to obtain atomic models when tubulin is involved. Here, we design and characterize new stathmin-like domain (SLD) proteins that sequester tubulins in numbers different from two, the number of tubulins bound by stathmin or by the SLD of RB3, two stathmin family members that have been extensively studied. We established rules for the design of tight tubulin-SLD assemblies and applied them to complexes containing one to four tubulin heterodimers. Biochemical and structural experiments showed that the engineered SLDs behaved as expected. The new SLDs will be tools for structural studies of microtubule regulation. The larger complexes will be useful for cryo-electron microscopy, whereas crystallography or nuclear magnetic resonance will benefit from the 1:1 tubulin-SLD assembly. Finally, our results provide new insight into SLD function, suggesting that a major effect of these phosphorylatable proteins is the programmed release of sequestered tubulin for microtubule assembly at the specific cellular locations of members of the stathmin family.

---

Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, Bâtiment 34, 1 avenue de la Terrasse, 91198 Gif sur Yvette, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A	451	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWZ0 (Ovis aries) Explore D0VWZ0  Go to UniProtKB:  D0VWZ0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B	445	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWY9 (Ovis aries) Explore D0VWY9  Go to UniProtKB:  D0VWY9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-like domain R1	C	87	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed ankyrin repeat protein (DARPIN) D2	D	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	E [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	H [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES	I [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.201 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.06	α = 90
b = 75.57	β = 96.29
c = 155.68	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-15 
• Released Date: 2012-07-18 
Deposition Author(s): Gigant, B., Mignot, I., Knossow, M.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references