3DU7

Tubulin-colchicine-phomopsin A: Stathmin-like domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into the inhibition of tubulin by vinca domain peptide ligands

Cormier, A.Marchand, M.Ravelli, R.B.Knossow, M.Gigant, B.

(2008) Embo Rep. 9: 1101-1106

  • DOI: 10.1038/embor.2008.171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The tubulin vinca domain is the target of widely different microtubule inhibitors that interfere with the binding of vinblastine. Although all these ligands inhibit the hydrolysis of GTP, they affect nucleotide exchange to variable extents. The struc ...

    The tubulin vinca domain is the target of widely different microtubule inhibitors that interfere with the binding of vinblastine. Although all these ligands inhibit the hydrolysis of GTP, they affect nucleotide exchange to variable extents. The structures of two vinca domain antimitotic peptides--phomopsin A and soblidotin (a dolastatin 10 analogue)--bound to tubulin in a complex with a stathmin-like domain show that their sites partly overlap with that of vinblastine and extend the definition of the vinca domain. The structural data, together with the biochemical results from the ligands we studied, highlight two main contributors in nucleotide exchange: the flexibility of the tubulin subunits' arrangement at their interfaces and the residues in the carboxy-terminal part of the beta-tubulin H6-H7 loop. The structures also highlight common features of the mechanisms by which vinca domain ligands favour curved tubulin assemblies and destabilize microtubules.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Bat. 34, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1C chain
A, C
449Bos taurusGene Names: TUBA1C
Find proteins for Q3ZCJ7 (Bos taurus)
Go to Gene View: TUBA1C
Go to UniProtKB:  Q3ZCJ7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-2B chain
B, D
445Bos taurusGene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Go to Gene View: TUBB2B
Go to UniProtKB:  Q6B856
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
142Rattus norvegicusGene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Go to UniProtKB:  P63043
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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Download CCD File 
D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
HOS
Query on HOS

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Download CCD File 
B, D
Phomopsin A
C36 H45 Cl N6 O12
FAFRRYBYQKPKSY-AJSRVUJESA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CN2
Query on CN2

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Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.215 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 327.126α = 90.00
b = 327.126β = 90.00
c = 53.672γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance