4DRX

GTP-Tubulin in complex with a DARPIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end.

Pecqueur, L.Duellberg, C.Dreier, B.Jiang, Q.Wang, C.Pluckthun, A.Surrey, T.Gigant, B.Knossow, M.

(2012) Proc.Natl.Acad.Sci.USA 109: 12011-12016

  • DOI: 10.1073/pnas.1204129109

  • PubMed Abstract: 
  • Microtubules are cytoskeleton filaments consisting of αβ-tubulin heterodimers. They switch between phases of growth and shrinkage. The underlying mechanism of this property, called dynamic instability, is not fully understood. Here, we identified a d ...

    Microtubules are cytoskeleton filaments consisting of αβ-tubulin heterodimers. They switch between phases of growth and shrinkage. The underlying mechanism of this property, called dynamic instability, is not fully understood. Here, we identified a designed ankyrin repeat protein (DARPin) that interferes with microtubule assembly in a unique manner. The X-ray structure of its complex with GTP-tubulin shows that it binds to the β-tubulin surface exposed at microtubule (+) ends. The details of the structure provide insight into the role of GTP in microtubule polymerization and the conformational state of tubulin at the very microtubule end. They show in particular that GTP facilitates the tubulin structural switch that accompanies microtubule assembly but does not trigger it in unpolymerized tubulin. Total internal reflection fluorescence microscopy revealed that the DARPin specifically blocks growth at the microtubule (+) end by a selective end-capping mechanism, ultimately favoring microtubule disassembly from that end. DARPins promise to become designable tools for the dissection of microtubule dynamic properties selective for either of their two different ends.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha chain
A, C
437Ovis aries
Find proteins for D0VWZ0 (Ovis aries)
Go to UniProtKB:  D0VWZ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, D
431Ovis aries
Find proteins for D0VWY9 (Ovis aries)
Go to UniProtKB:  D0VWY9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Designed ankyrin repeat protein (DARPIN) D1
E, F
169N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.884α = 90.00
b = 90.596β = 90.02
c = 117.575γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-08
    Type: Database references