3J6E

Energy minimized average structure of Microtubules stabilized by GmpCpp

• PDB DOI:  https://doi.org/10.2210/pdb3J6E/pdb
• EM Map EMD-5895: EMDB EMDataResource

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


• Deposited: 2014-02-18 Released: 2014-06-04 
• Deposition Author(s): Alushin, G.M., Lander, G.C., Kellogg, E.H., Zhang, R., Baker, D., Nogales, E.

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Experimental Data Snapshot

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

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

• PubMed: 24855948 
• 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.

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Organizational Affiliation: 

Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Hetero 18-mer - A9B9 Pseudo Symmetry: Helical - H  (3D View)
Pseudo Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 880.24 kDa 
• Atom Count: 60,984 
• Modelled Residue Count: 7,686 
• Deposited Residue Count: 7,794 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A, C, E, G, I, K, M, O, Q	439	Sus scrofa	Mutation(s): 0  Gene Names: TUBA1A
UniProt
Find proteins for P02550 (Sus scrofa) Explore P02550  Go to UniProtKB:  P02550

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D, F, H, J, L, N, P, R	427	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554  Go to UniProtKB:  P02554

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	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	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	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:

Task	Software Package	Version
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	SPARX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Alushin, G.M., Lander, G.C., Kellogg, E.H., Zhang, R., Baker, D., Nogales, E.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Author supporting evidence, Data collection