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 1.3 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chain
A, C
451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2HJ86 (Bos taurus)
Explore Q2HJ86 
Go to UniProtKB:  Q2HJ86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2HJ86
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin 4142Rattus 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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / 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
GDP
Query on GDP

Download Ideal Coordinates CCD File 
I [auth B],
M [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
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
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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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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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description