6GWC | pdb_00006gwc

Tubulin:iE5 alphaRep complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.223 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6GWC

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Selection and Characterization of Artificial Proteins Targeting the Tubulin alpha Subunit.

Campanacci, V.Urvoas, A.Consolati, T.Cantos-Fernandes, S.Aumont-Nicaise, M.Valerio-Lepiniec, M.Surrey, T.Minard, P.Gigant, B.

(2019) Structure 27: 497-506.e4

  • DOI: https://doi.org/10.1016/j.str.2018.12.001
  • Primary Citation Related Structures: 
    6GWC, 6GWD

  • PubMed Abstract: 

    Microtubules are cytoskeletal filaments of eukaryotic cells made of αβ-tubulin heterodimers. Structural studies of non-microtubular tubulin rely mainly on molecules that prevent its self-assembly and are used as crystallization chaperones. Here we identified artificial proteins from an αRep library that are specific to α-tubulin. Turbidity experiments indicate that these αReps impede microtubule assembly in a dose-dependent manner and total internal reflection fluorescence microscopy further shows that they specifically block growth at the microtubule (-) end. Structural data indicate that they do so by targeting the α-tubulin longitudinal surface. Interestingly, in one of the complexes studied, the α subunit is in a conformation that is intermediate between the ones most commonly observed in X-ray structures of tubulin and those seen in the microtubule, emphasizing the plasticity of tubulin. These α-tubulin-specific αReps broaden the range of tools available for the mechanistic study of microtubule dynamics and its regulation.


  • Organizational Affiliation
    • Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.

Macromolecule Content 

  • Total Structure Weight: 127.01 kDa 
  • Atom Count: 8,478 
  • Modeled Residue Count: 1,065 
  • Deposited Residue Count: 1,128 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALPHA-TUBULIN451Ovis ariesMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain445Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWY9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
iE5 ALPHAREP232synthetic constructMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
I [auth B],
J [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.223 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.346α = 90
b = 102.346β = 90
c = 216.207γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description