3UT5

Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural plasticity of tubulin assembly probed by vinca-domain ligands.

Ranaivoson, F.M.Gigant, B.Berritt, S.Joullie, M.Knossow, M.

(2012) Acta Crystallogr D Biol Crystallogr 68: 927-934

  • DOI: 10.1107/S0907444912017143
  • Primary Citation of Related Structures:  
    4EB6, 3UT5

  • PubMed Abstract: 
  • Vinca-domain ligands are compounds that bind to tubulin at its inter-heterodimeric interface and favour heterogeneous protofilament-like assemblies, giving rise to helices and rings. This is the basis for their inhibition of microtubule assembly, for their antimitotic activities and for their use in anticancer chemotherapy ...

    Vinca-domain ligands are compounds that bind to tubulin at its inter-heterodimeric interface and favour heterogeneous protofilament-like assemblies, giving rise to helices and rings. This is the basis for their inhibition of microtubule assembly, for their antimitotic activities and for their use in anticancer chemotherapy. Ustiloxins are vinca-domain ligands with a well established total synthesis. A 2.7 Å resolution structure of ustiloxin D bound to the vinca domain embedded in the complex of two tubulins with the stathmin-like domain of RB3 (T(2)R) has been determined. This finding precisely defines the interactions of ustiloxins with tubulin and, taken together with structures of other vinca-ligand complexes, allows structure-based suggestions to be made for improved activity. These comparisons also provide a rationale for the large-scale polymorphism of the protofilament-like assemblies mediated by vinca-domain ligands based on local differences in their interactions with the two tubulin heterodimers constituting their binding site.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 91198 Gif-sur-Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chainA, C451Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWZ0 (Ovis aries)
Explore D0VWZ0 
Go to UniProtKB:  D0VWZ0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB, D445Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E142Rattus norvegicusMutation(s): 2 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Vinca tetrapeptideF4N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

Download Ideal Coordinates CCD File 
K [auth B], P [auth D]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
LOC
Query on LOC

Download Ideal Coordinates CCD File 
L [auth B], Q [auth D]N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
C22 H25 N O6
IAKHMKGGTNLKSZ-INIZCTEOSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], M [auth B], R [auth D], S [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A], O [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0E5
Query on 0E5
FL-PEPTIDE LINKINGC6 H13 N O3THR
0EA
Query on 0EA
FL-PEPTIDE LINKINGC10 H13 N O5TYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LOCIC50:  1060   nM  BindingDB
LOCIC50:  6.699999809265137   nM  BindingDB
LOCIC50:  4168.68994140625   nM  BindingDB
LOCIC50:  1260   nM  BindingDB
LOCIC50:  800   nM  BindingDB
LOCIC50:  1400   nM  BindingDB
LOCIC50:  29300   nM  BindingDB
LOCIC50:  3500   nM  BindingDB
LOCIC50:  7850   nM  BindingDB
LOCIC50:  2400   nM  BindingDB
LOCIC50:  2620   nM  BindingDB
LOCIC50:  10000   nM  BindingDB
LOCIC50:  1900   nM  BindingDB
LOCKi:  1.600000023841858   nM  BindingDB
LOCIC50:  1500   nM  BindingDB
LOCIC50:  1700   nM  BindingDB
LOCKi:  5750   nM  BindingDB
LOCIC50:  1900   nM  BindingDB
LOCIC50:  6930   nM  BindingDB
LOCKi:  2500   nM  BindingDB
LOCIC50:  2100   nM  BindingDB
LOCIC50:  800   nM  BindingDB
LOCKi:  780   nM  BindingDB
LOCIC50:  2680   nM  BindingDB
LOCIC50:  3790   nM  BindingDB
LOCKd:  3700   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.81α = 90
b = 128.87β = 90
c = 254.84γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2013-01-23
    Changes: Database references