Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 101.11 kDa 
• Atom Count: 6515 
• Residue Count: 820 
• Unique protein chains: 2

3J7I

Structure of alpha- and beta- tubulin in GMPCPP-microtubules

• DOI: 10.2210/pdb3J7I/pdb
• EMDataResource: EMD-2697

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


• Deposited: 2014-07-01 Released: 2014-12-10 
• Deposition Author(s): Yajima, H., Ogura, T., Nitta, R., Okada, Y., Sato, C., Hirokawa, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.90 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Conformational changes in tubulin in GMPCPP and GDP-taxol microtubules observed by cryoelectron microscopy

Yajima, H., Ogura, T., Nitta, R., Okada, Y., Sato, C., Hirokawa, N.

(2012) J Cell Biol 198: 315-322

• PubMed: 22851320 
• DOI: 10.1083/jcb.201201161
• Primary Citation of Related Structures:  
  3J7I


• PubMed Abstract: 
  

Microtubules are dynamic polymers that stochastically switch between growing and shrinking phases. Microtubule dynamics are regulated by guanosine triphosphate (GTP) hydrolysis by β-tubulin, but the mechanism of this regulation remains elusive because high-resolution microtubule structures have only been revealed for the guanosine diphosphate (GDP) state. In this paper, we solved the cryoelectron microscopy (cryo-EM) structure of microtubule stabilized with a GTP analogue, guanylyl 5'-α,β-methylenediphosphonate (GMPCPP), at 8.8-Å resolution by developing a novel cryo-EM image reconstruction algorithm. In contrast to the crystal structures of GTP-bound tubulin relatives such as γ-tubulin and bacterial tubulins, significant changes were detected between GMPCPP and GDP-taxol microtubules at the contacts between tubulins both along the protofilament and between neighboring protofilaments, contributing to the stability of the microtubule. These findings are consistent with the structural plasticity or lattice model and suggest the structural basis not only for the regulatory mechanism of microtubule dynamics but also for the recognition of the nucleotide state of the microtubule by several microtubule-binding proteins, such as EB1 or kinesin.

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Related Citations: 

• Mutual Conformational Changes of Kinesin and GTP-Microtubule Upon their Binding
  Yajima, H., Ogura, T., Nitta, R., Okada, Y., Sato, C., Hirokawa, N.
  () To be published --: --

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Organizational Affiliation: 

Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A	451	Sus scrofa	Mutation(s): 0  Gene Names: TUBA1A
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	445	Sus scrofa	Mutation(s): 0
Find proteins for P02554 (Sus scrofa) Explore P02554  Go to UniProtKB:  P02554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	A, B	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.90 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-01 
• Released Date: 2014-12-10 
Deposition Author(s): Yajima, H., Ogura, T., Nitta, R., Okada, Y., Sato, C., Hirokawa, N.

Revision History 

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Data collection, Database references