6EW0 | pdb_00006ew0

Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin and supplemented with Taxol

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2017-11-03 Released: 2018-07-04 
  • Deposition Author(s): Manka, S.W.
  • Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EW0

This is version 1.4 of the entry. See complete history

Literature

The role of tubulin-tubulin lattice contacts in the mechanism of microtubule dynamic instability.

Manka, S.W.Moores, C.A.

(2018) Nat Struct Mol Biol 25: 607-615

  • DOI: https://doi.org/10.1038/s41594-018-0087-8
  • Primary Citation Related Structures: 
    6EVW, 6EVX, 6EVY, 6EVZ, 6EW0

  • PubMed Abstract: 

    Microtubules form from longitudinally and laterally assembling tubulin α-β dimers. The assembly induces strain in tubulin, resulting in cycles of microtubule catastrophe and regrowth. This 'dynamic instability' is governed by GTP hydrolysis that renders the microtubule lattice unstable, but it is unclear how. We used a human microtubule nucleating and stabilizing neuronal protein, doublecortin, and high-resolution cryo-EM to capture tubulin's elusive hydrolysis intermediate GDP•Pi state, alongside the prehydrolysis analog GMPCPP state and the posthydrolysis GDP state with and without an anticancer drug, Taxol. GTP hydrolysis to GDP•Pi followed by Pi release constitutes two distinct structural transitions, causing unevenly distributed compressions of tubulin dimers, thereby tightening longitudinal and loosening lateral interdimer contacts. We conclude that microtubule catastrophe is triggered because the lateral contacts can no longer counteract the strain energy stored in the lattice, while reinforcement of the longitudinal contacts may support generation of force.


  • Organizational Affiliation
    • Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK. s.manka@mail.cryst.bbk.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 611.74 kDa 
  • Atom Count: 41,238 
  • Modeled Residue Count: 5,166 
  • Deposited Residue Count: 5,376 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02554
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1

Query on TA1



Download:Ideal Coordinates CCD File
AA [auth G]
CA [auth D]
EA [auth I]
GA [auth B]
IA [auth H]
AA [auth G],
CA [auth D],
EA [auth I],
GA [auth B],
IA [auth H],
P [auth F]
TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP

Query on GTP



Download:Ideal Coordinates CCD File
M [auth E]
Q [auth J]
S [auth C]
U [auth L]
W [auth A]
M [auth E],
Q [auth J],
S [auth C],
U [auth L],
W [auth A],
Y [auth K]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
BA [auth G]
DA [auth D]
FA [auth I]
HA [auth B]
JA [auth H]
BA [auth G],
DA [auth D],
FA [auth I],
HA [auth B],
JA [auth H],
O [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
N [auth E]
R [auth J]
T [auth C]
V [auth L]
X [auth A]
N [auth E],
R [auth J],
T [auth C],
V [auth L],
X [auth A],
Z [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2018-07-04 
  • Deposition Author(s): Manka, S.W.

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references, Derived calculations