Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Hetero 18-mer - A9B9 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 876.95 kDa 
• Atom Count: 60903 
• Residue Count: 7686 
• Unique protein chains: 2

5XXW

GDP-microtubule complexed with KIF5C in ATP state

• DOI: 10.2210/pdb5XXW/pdb
• EMDataResource: EMD-6782

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


• Deposited: 2017-07-05 Released: 2018-10-10 
• Deposition Author(s): Morikawa, M., Shigematsu, H., Nitta, R., Hirokawa, N.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport

Shima, T., Morikawa, M., Kaneshiro, J., Kambara, T., Kamimura, S., Yagi, T., Iwamoto, H., Uemura, S., Shigematsu, H., Shirouzu, M., Ichimura, T., Watanabe, T.M., Nitta, R., Okada, Y., Hirokawa, N.

(2018) J Cell Biol 217: 4164-4183

• PubMed: 30297389 
• DOI: 10.1083/jcb.201711178
• Primary Citation of Related Structures:  
  5XXT, 5XXV, 5XXX, 5XXW


• PubMed Abstract: 
  

Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule.

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Organizational Affiliation: 

Center of Excellence in Genome Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A,  C,  E,  G,  I,  K,  M,  O,  Q	438	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,  D,  F,  H,  J,  L,  N,  P,  R	426	Sus scrofa	Mutation(s): 0
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	A, C, E, G, I, K, M, O, Q	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	B, D, F, H, J, L, N, P, R	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	A, C, E, G, I, K, M, O, Q	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-05 
• Released Date: 2018-10-10 
Deposition Author(s): Morikawa, M., Shigematsu, H., Nitta, R., Hirokawa, N.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	23000013
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	16H06372
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	17H05897
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	15K08168

Revision History 

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2018-12-19
  Changes: Data collection, Database references
• Version 1.3: 2019-11-06
  Changes: Data collection, Other