1Z2B

Tubulin-colchicine-vinblastine: stathmin-like domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the regulation of tubulin by vinblastine.

Gigant, B.Wang, C.Ravelli, R.B.Roussi, F.Steinmetz, M.O.Curmi, P.A.Sobel, A.Knossow, M.

(2005) Nature 435: 519-522

  • DOI: https://doi.org/10.1038/nature03566
  • Primary Citation of Related Structures:  
    1Z2B

  • PubMed Abstract: 

    Vinblastine is one of several tubulin-targeting Vinca alkaloids that have been responsible for many chemotherapeutic successes since their introduction in the clinic as antitumour drugs. In contrast with the two other classes of small tubulin-binding molecules (Taxol and colchicine), the binding site of vinblastine is largely unknown and the molecular mechanism of this drug has remained elusive. Here we report the X-ray structure of vinblastine bound to tubulin in a complex with the RB3 protein stathmin-like domain (RB3-SLD). Vinblastine introduces a wedge at the interface of two tubulin molecules and thus interferes with tubulin assembly. Together with electron microscopical and biochemical data, the structure explains vinblastine-induced tubulin self-association into spiral aggregates at the expense of microtubule growth. It also shows that vinblastine and the amino-terminal part of RB3-SLD binding sites share a hydrophobic groove on the alpha-tubulin surface that is located at an intermolecular contact in microtubules. This is an attractive target for drugs designed to perturb microtubule dynamics by interfacial interference, for which tubulin seems ideally suited because of its propensity to self-associate.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063, Centre National de la Recherche Scientifique, Bâtiment 34, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chain
A, C
448Bos taurusMutation(s): 0 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B856
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RB3 STATHMIN-LIKE DOMAIN 4142Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63043
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VLB
Query on VLB

Download Ideal Coordinates CCD File 
L [auth C](2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE
C46 H58 N4 O9
JXLYSJRDGCGARV-CFWMRBGOSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
H [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 
I [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],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VLB PDBBind:  1Z2B Kd: 400 (nM) from 1 assay(s)
BindingDB:  1Z2B IC50: min: 600, max: 700 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 324.852α = 90
b = 324.852β = 90
c = 54.208γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description