Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48547.29 
• Atom Count: 2898 
• Residue Count: 420 
• Unique protein chains: 1

2NCD

NCD (NON-CLARET DISJUNCTIONAL) DIMER FROM D. MELANOGASTER

• DOI: 10.2210/pdb2NCD/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli


• Deposited: 1999-06-04 Released: 1999-06-09 
• Deposition Author(s): Sablin, E.P., Case, R.B., Dai, S.C., Hart, C.L., Ruby, A., Vale, R.D., Fletterick, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 

Literature

Direction determination in the minus-end-directed kinesin motor ncd.

Sablin, E.P., Case, R.B., Dai, S.C., Hart, C.L., Ruby, A., Vale, R.D., Fletterick, R.J.

(1998) Nature 395: 813-816

• PubMed: 9796817 
• DOI: 10.1038/27463


• PubMed Abstract: 
  

Motor proteins of the kinesin superfamily transport intracellular cargo along microtubules. Although different kinesin proteins share 30-50% amino-acid identity in their motor catalytic cores, some move to the plus end of microtubules whereas others travel in the opposite direction. Crystal structures of the catalytic cores of conventional kinesin (a plus-end-directed motor involved in organelle transport) and ncd (a minus-end-directed motor involved in chromosome segregation) are nearly identical; therefore, the structural basis for their opposite directions of movement is unknown. Here we show that the ncd 'neck' made up of 13 class-specific residues next to the superfamily-conserved catalytic core, is essential for minus-end-directed motility, as mutagenesis of these neck residues reverses the direction of ncd motion. By solving the 2.5 A structure of a functional ncd dimer, we show that the ncd neck (a coiled-coil) differs from the corresponding region in the kinesin neck (an interrupted beta-strand), although both necks interact with similar elements in the catalytic cores. The distinct neck architectures also confer different symmetries to the ncd and kinesin dimers and position these motors with appropriate directional bias on the microtubule.

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Organizational Affiliation: 

Department of Biochemistry/Biophysics, University of California, San Francisco 94143, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (Kinesin motor NCD)	A	420	Drosophila melanogaster	Mutation(s): 0  Gene Names: ncd (CA(ND))
Find proteins for P20480 (Drosophila melanogaster) Go to UniProtKB:  P20480

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 123.000	α = 90.00
b = 123.000	β = 90.00
c = 121.100	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-06-04 
• Released Date: 1999-06-09 
• Deposition Author(s): Sablin, E.P., Case, R.B., Dai, S.C., Hart, C.L., Ruby, A., Vale, R.D., Fletterick, R.J.

Revision History 

• Version 1.0: 1999-06-09
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance