8YUE | pdb_00008yue

Crystal structure of the kinesin-14 motor protein from Drosophila melanogaster

• PDB DOI: https://doi.org/10.2210/pdb8YUE/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-03-27 Released: 2025-04-09 
• Deposition Author(s): Wei, Y., Jobichen, C., Imasaki, T., Nitta, R., Wang, M.Y., Sivaraman, J., Endow, S.A.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.295 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a kinesin-related protein from Drosophila melanogaster

Shibata, S., Wang, M.Y., Imasaki, T., Shigematsu, H., Wei, Y., Jobichen, C., Hagio, H., Sivaraman, J., Endow, S.A., Nitta, R.

To be published.

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: 90.15 kDa 
• Atom Count: 5,793 
• Modeled Residue Count: 721 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein claret segregational	A, B	390	Drosophila melanogaster	Mutation(s): 1  Gene Names: ncd, CA(ND), CG7831 EC: 3.6.4
UniProt
Find proteins for P20480 (Drosophila melanogaster) Explore P20480  Go to UniProtKB:  P20480

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)	D [auth A], E [auth A], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.295 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.506	α = 90
b = 67.617	β = 96.99
c = 94.196	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Wei, Y., Jobichen, C., Imasaki, T., Nitta, R., Wang, M.Y., Sivaraman, J., Endow, S.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	1R21HD105034-01A1

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release