Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129788.10 
• Atom Count: 8524 
• Residue Count: 1152 
• Unique protein chains: 4

4F6R

Tubulin:Stathmin-like domain complex

• DOI: 10.2210/pdb4F6R/pdb

• Classification: CELL CYCLE
• Organism(s): Ovis aries
• Expression System: Escherichia coli BL21(DE3), Escherichia coli


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

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Experimental Data Snapshot

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

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


• 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.

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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

Find similar proteins by: Sequence  |  Structure

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

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Stathmin-like domain R1	C	87	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Designed ankyrin repeat protein (DARPIN) D2	D	169	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	B	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GTP	A	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-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 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 95.060	α = 90.00
b = 75.570	β = 96.29
c = 155.680	γ = 90.00

Software Package:

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

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
  Type: Database references