3U06

Crystal structure of the kinesin-14 NcdG347D

• PDB DOI: https://doi.org/10.2210/pdb3U06/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-09-28 Released: 2012-03-07 
• Deposition Author(s): Liu, H.-L., Pemble IV, C.W., Endow, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.250 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

Neck-motor interactions trigger rotation of the kinesin stalk.

Liu, H.L., Pemble Iv, C.W., Endow, S.A.

(2012) Sci Rep 2: 236-236

• PubMed: 22355749 
• DOI: https://doi.org/10.1038/srep00236
• Primary Citation of Related Structures:  
  3U06


• PubMed Abstract: 
  

  Rotation of the coiled-coil stalk of the kinesin-14 motors is thought to drive displacements or steps by the motor along microtubules, but the structural changes that trigger stalk rotation and the nucleotide state in which it occurs are not certain. Here we report a kinesin-14 neck mutant that releases ADP more slowly than wild type and shows weaker microtubule affinity, consistent with defective stalk rotation. Unexpectedly, crystal structures show the stalk fully rotated - neck-motor interactions destabilize the stalk, causing it to rotate and ADP to be released, and alter motor affinity for microtubules. A new structural pathway accounts for the coupling of stalk rotation - the force-producing stroke - to changes in motor affinity for nucleotide and microtubules. Sequential disruption of salt bridges that stabilize the unrotated stalk could cause the stalk to initiate and complete rotation in different nucleotide states.

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Organizational Affiliation: 

Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.92 kDa 
• Atom Count: 5,836 
• Modelled Residue Count: 703 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein claret segregational	A, B	412	Drosophila melanogaster	Mutation(s): 1  Gene Names: CA(ND), CG7831, ncd, non-claret disjunctional
UniProt
Find proteins for P20480 (Drosophila melanogaster) Explore P20480  Go to UniProtKB:  P20480

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.250 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.539	α = 90
b = 67.094	β = 98.91
c = 94.369	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Liu, H.-L., Pemble IV, C.W., Endow, S.A.

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations