3J6E

Energy minimized average structure of Microtubules stabilized by GmpCpp


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-Resolution Microtubule Structures Reveal the Structural Transitions in alpha beta-Tubulin upon GTP Hydrolysis.

Alushin, G.M.Lander, G.C.Kellogg, E.H.Zhang, R.Baker, D.Nogales, E.

(2014) Cell 157: 1117-1129

  • DOI: https://doi.org/10.1016/j.cell.2014.03.053
  • Primary Citation of Related Structures:  
    3J6E, 3J6F, 3J6G

  • PubMed Abstract: 

    Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is inhibited by anticancer agents like Taxol. We provide insight into the mechanism of dynamic instability, based on high-resolution cryo-EM structures (4.7-5.6 Å) of dynamic microtubules and microtubules stabilized by GMPCPP or Taxol. We infer that hydrolysis leads to a compaction around the E-site nucleotide at longitudinal interfaces, as well as movement of the α-tubulin intermediate domain and H7 helix. Displacement of the C-terminal helices in both α- and β-tubulin subunits suggests an effect on interactions with binding partners that contact this region. Taxol inhibits most of these conformational changes, allosterically inducing a GMPCPP-like state. Lateral interactions are similar in all conditions we examined, suggesting that microtubule lattice stability is primarily modulated at longitudinal interfaces.


  • Organizational Affiliation

    Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chain
A, C, E, G, I
A, C, E, G, I, K, M, O, Q
439Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02550
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D, F, H, J
B, D, F, H, J, L, N, P, R
427Sus 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth G]
IA [auth I]
MA [auth K]
QA [auth M]
AA [auth E],
EA [auth G],
IA [auth I],
MA [auth K],
QA [auth M],
S [auth A],
UA [auth O],
W [auth C],
YA [auth Q]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
G2P
Query on G2P

Download Ideal Coordinates CCD File 
AB [auth R]
CA [auth F]
GA [auth H]
KA [auth J]
OA [auth L]
AB [auth R],
CA [auth F],
GA [auth H],
KA [auth J],
OA [auth L],
SA [auth N],
U [auth B],
WA [auth P],
Y [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E]
BB [auth R]
DA [auth F]
FA [auth G]
HA [auth H]
BA [auth E],
BB [auth R],
DA [auth F],
FA [auth G],
HA [auth H],
JA [auth I],
LA [auth J],
NA [auth K],
PA [auth L],
RA [auth M],
T [auth A],
TA [auth N],
V [auth B],
VA [auth O],
X [auth C],
XA [auth P],
Z [auth D],
ZA [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONSPARX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description