1SA0

TUBULIN-COLCHICINE: STATHMIN-LIKE DOMAIN COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1038/nature02393
  • Primary Citation of Related Structures:  
    1SA0, 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chainA, C451Bos taurusMutation(s): 0 
Gene Names: TUBA1D
UniProt
Find proteins for Q2HJ86 (Bos taurus)
Explore Q2HJ86 
Go to UniProtKB:  Q2HJ86
Entity Groups  
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UniProt GroupQ2HJ86
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB, D445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin 4E142Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups  
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UniProt GroupP63043
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
G [auth A],
L [auth C]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
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I [auth B],
M [auth D]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
CN2
Query on CN2
Download Ideal Coordinates CCD File 
J [auth B],
N [auth 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		 Ligand Interaction
MG
Query on MG
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F [auth A],
H [auth B],
K [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 328.69α = 90
b = 328.691β = 90
c = 54.679γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMmodel building
REFMACrefinement
DMphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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