Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer -A4B 

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

Macromolecule Content

• Total Structure Weight: 219723.88 
• Atom Count: 14074 
• Residue Count: 1934 
• Unique protein chains: 3

1SA0

TUBULIN-COLCHICINE: STATHMIN-LIKE DOMAIN COMPLEX

• DOI: 10.2210/pdb1SA0/pdb

• Classification: CELL CYCLE
• Organism(s): Bos taurus, Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-02-06 Released: 2004-03-23 
• Deposition Author(s): Ravelli, R.B., Gigant, B., Curmi, P.A., Jourdain, I., Lachkar, S., Sobel, A., Knossow, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 0.249 
• R-Value Work: 0.232 

Literature

Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain.

Ravelli, R.B., Gigant, B., Curmi, P.A., Jourdain, I., Lachkar, S., Sobel, A., Knossow, M.

(2004) Nature 428: 198-202

• PubMed: 15014504 
• DOI: 10.1038/nature02393
• Primary Citation of Related Structures:  
  1SA1


• PubMed Abstract: 
  

Microtubules are cytoskeletal polymers of tubulin involved in many cellular functions. Their dynamic instability is controlled by numerous compounds and proteins, including colchicine and stathmin family proteins. The way in which microtubule instability is regulated at the molecular level has remained elusive, mainly because of the lack of appropriate structural data. Here, we present the structure, at 3.5 A resolution, of tubulin in complex with colchicine and with the stathmin-like domain (SLD) of RB3. It shows the interaction of RB3-SLD with two tubulin heterodimers in a curved complex capped by the SLD amino-terminal domain, which prevents the incorporation of the complexed tubulin into microtubules. A comparison with the structure of tubulin in protofilaments shows changes in the subunits of tubulin as it switches from its straight conformation to a curved one. These changes correlate with the loss of lateral contacts and provide a rationale for the rapid microtubule depolymerization characteristic of dynamic instability. Moreover, the tubulin-colchicine complex sheds light on the mechanism of colchicine's activity: we show that colchicine binds at a location where it prevents curved tubulin from adopting a straight structure, which inhibits assembly.

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Organizational Affiliation: 

European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, BP 181, 38042 Grenoble Cedex 9, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tubulin alpha chain	A, C	451	Bos taurus	Mutation(s): 0  Gene Names: TUBA1D
Find proteins for Q2HJ86 (Bos taurus) Go to UniProtKB:  Q2HJ86

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Tubulin beta chain	B, D	445	Bos taurus	Mutation(s): 0  Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus) Go to Gene View: TUBB2B Go to UniProtKB:  Q6B856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Stathmin 4	E	142	Rattus norvegicus	Mutation(s): 0  Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus) Go to UniProtKB:  P63043

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	B, D	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GTP	A, C	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	A, B, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
CN2	B, D	2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE C22 H25 N O6 S TYDIWMTWTXFWSY-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 0.249 
• R-Value Work: 0.232 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 328.690	α = 90.00
b = 328.691	β = 90.00
c = 54.679	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
SHELXD	phasing
REFMAC	refinement
DM	phasing
SHARP	phasing
DM	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-06 
• Released Date: 2004-03-23 
• Deposition Author(s): Ravelli, R.B., Gigant, B., Curmi, P.A., Jourdain, I., Lachkar, S., Sobel, A., Knossow, M.

Revision History 

• Version 1.0: 2004-03-23
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance