1RY6 | pdb_00001ry6

Crystal Structure of Internal Kinesin Motor Domain

• PDB DOI: https://doi.org/10.2210/pdb1RY6/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-19 Released: 2004-04-13 
• Deposition Author(s): Shipley, K., Hekmat-Nejad, M., Turner, J., Moores, C., Anderson, R., Milligan, R., Sakowicz, R., Fletterick, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.231 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of a kinesin microtubule depolymerization machine.

Shipley, K., Hekmat-Nejad, M., Turner, J., Moores, C., Anderson, R., Milligan, R., Sakowicz, R., Fletterick, R.

(2004) EMBO J 23: 1422-1432

• PubMed: 15029249 
• DOI: https://doi.org/10.1038/sj.emboj.7600165
• Primary Citation Related Structures: 
  1RY6


• PubMed Abstract: 
  

  With their ability to depolymerize microtubules (MTs), KinI kinesins are the rogue members of the kinesin family. Here we present the 1.6 A crystal structure of a KinI motor core from Plasmodium falciparum, which is sufficient for depolymerization in vitro. Unlike all published kinesin structures to date, nucleotide is not present, and there are noticeable differences in loop regions L6 and L10 (the plus-end tip), L2 and L8 and in switch II (L11 and helix4); otherwise, the pKinI structure is very similar to previous kinesin structures. KinI-conserved amino acids were mutated to alanine, and studied for their effects on depolymerization and ATP hydrolysis. Notably, mutation of three residues in L2 appears to primarily affect depolymerization, rather than general MT binding or ATP hydrolysis. The results of this study confirm the suspected importance of loop 2 for KinI function, and provide evidence that KinI is specialized to hydrolyze ATP after initiating depolymerization.

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Organizational Affiliation: 
• Graduate Group in Biophysics, University of California, San Francisco, CA, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.86 kDa 
• Atom Count: 2,829 
• Modeled Residue Count: 319 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERNAL KINESIN	A	360	Plasmodium falciparum	Mutation(s): 0  Gene Names: PFL2165W
UniProt
Find proteins for Q8I4Y0 (Plasmodium falciparum (isolate 3D7)) Explore Q8I4Y0  Go to UniProtKB:  Q8I4Y0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.231 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.588	α = 90
b = 105.588	β = 90
c = 84.771	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-13 
Deposition Author(s): Shipley, K., Hekmat-Nejad, M., Turner, J., Moores, C., Anderson, R., Milligan, R., Sakowicz, R., Fletterick, R.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description