1VFW | pdb_00001vfw

Crystal Structure of the Kif1A Motor Domain Complexed With Mg-AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb1VFW/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-04-19 Released: 2004-08-10 
• Deposition Author(s): Nitta, R., Kikkawa, M., Okada, Y., Hirokawa, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

KIF1A Alternately Uses Two Loops to Bind Microtubules

Nitta, R., Kikkawa, M., Okada, Y., Hirokawa, N.

(2004) Science 305: 678-683

• PubMed: 15286375 
• DOI: https://doi.org/10.1126/science.1096621
• Primary Citation Related Structures: 
  1VFV, 1VFW, 1VFX, 1VFZ


• PubMed Abstract: 
  

  The motor protein kinesin moves along microtubules, driven by adenosine triphosphate (ATP) hydrolysis. However, it remains unclear how kinesin converts the chemical energy into mechanical movement. We report crystal structures of monomeric kinesin KIF1A with three transition-state analogs: adenylyl imidodiphosphate (AMP-PNP), adenosine diphosphate (ADP)-vanadate, and ADP-AlFx (aluminofluoride complexes). These structures, together with known structures of the ADP-bound state and the adenylyl-(beta,gamma-methylene) diphosphate (AMP-PCP)-bound state, show that kinesin uses two microtubule-binding loops in an alternating manner to change its interaction with microtubules during the ATP hydrolysis cycle; loop L11 is extended in the AMP-PNP structure, whereas loop L12 is extended in the ADP structure. ADP-vanadate displays an intermediate structure in which a conformational change in two switch regions causes both loops to be raised from the microtubule, thus actively detaching kinesin.

---

Organizational Affiliation: 
• Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.66 kDa 
• Atom Count: 2,819 
• Modeled Residue Count: 329 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Fusion protein consisting of Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C and A HIS TAG	A	366	Mus musculus	Mutation(s): 0  EC: 5.6.1.3
UniProt
Find proteins for P33173 (Mus musculus) Explore P33173  Go to UniProtKB:  P33173

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.64	α = 90
b = 55.48	β = 90
c = 156.71	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Nitta, R., Kikkawa, M., Okada, Y., Hirokawa, N.

Revision History  

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-23
  Changes: Source and taxonomy
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations