Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 146627.98 
• Atom Count: 9388 
• Residue Count: 1290 
• Unique protein chains: 3

2HXH

KIF1A head-microtubule complex structure in adp-form

• DOI: 10.2210/pdb2HXH/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus, Sus scrofa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2006-08-03 Released: 2006-10-10 
• Deposition Author(s): Kikkawa, M., Hirokawa, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 11 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations

Kikkawa, M., Hirokawa, N.

(2006) Embo J. 25: 4187-4194

• PubMed: 16946706 
• DOI: 10.1038/sj.emboj.7601299
• Primary Citation of Related Structures:  
  2HXF


• PubMed Abstract: 
  

Kinesin is an ATP-driven microtubule (MT)-based motor fundamental to organelle transport. Although a number of kinesin crystal structures have been solved, the structural evidence for coupling between the bound nucleotide and the conformation of kinesin is elusive. In addition, the structural basis of the MT-induced ATPase activity of kinesin is not clear because of the absence of the MT in the structure. Here, we report cryo-electron microscopy structures of the monomeric kinesin KIF1A-MT complex in two nucleotide states at about 10 A resolution, sufficient to reveal the secondary structure. These high-resolution maps visualized clear structural changes that suggest a mechanical pathway from the nucleotide to the neck linker via the motor core rotation. In addition, new nucleotide binding pocket conformations are observed that are different from X-ray crystallographic structures; it is closed in the 5'-adenylyl-imidodiphosphate state, but open in the ADP state. These results suggest a structural model of biased diffusion movement of monomeric kinesin motor.

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Organizational Affiliation: 

Department of Cell Biology, Southwestern Medical Center, University of Texas, Dallas, TX, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tubulin alpha chain	A	451	Sus scrofa	Mutation(s): 0  Gene Names: TUBA1A
Find proteins for P02550 (Sus scrofa) Go to Gene View: TUBA1A Go to UniProtKB:  P02550

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Tubulin beta chain	B	445	Sus scrofa	Mutation(s): 0
Find proteins for P02554 (Sus scrofa) Go to UniProtKB:  P02554

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Kinesin-like protein KIF1A	C	394	Mus musculus	Mutation(s): 1  Gene Names: Kif1a (Atsv, Kif1)
Find proteins for P33173 (Mus musculus) Go to UniProtKB:  P33173

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	B	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP	C	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GTP	A	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	A, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
TA1	B	TAXOL C47 H51 N O14 RCINICONZNJXQF-MZXODVADSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 11 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-03 
• Released Date: 2006-10-10 
• Deposition Author(s): Kikkawa, M., Hirokawa, N.

Revision History 

• Version 1.0: 2006-10-10
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance