3DC4

Crystal structure of the Drosophila kinesin family member NOD in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement.

Cochran, J.C.Sindelar, C.V.Mulko, N.K.Collins, K.A.Kong, S.E.Hawley, R.S.Kull, F.J.

(2009) Cell 136: 110-122

  • DOI: https://doi.org/10.1016/j.cell.2008.11.048
  • Primary Citation of Related Structures:  
    3DC4, 3DCB, 3DCO

  • PubMed Abstract: 

    Segregation of nonexchange chromosomes during Drosophila melanogaster meiosis requires the proper function of NOD, a nonmotile kinesin-10. We have determined the X-ray crystal structure of the NOD catalytic domain in the ADP- and AMPPNP-bound states. These structures reveal an alternate conformation of the microtubule binding region as well as a nucleotide-sensitive relay of hydrogen bonds at the active site. Additionally, a cryo-electron microscopy reconstruction of the nucleotide-free microtubule-NOD complex shows an atypical binding orientation. Thermodynamic studies show that NOD binds tightly to microtubules in the nucleotide-free state, yet other nucleotide states, including AMPPNP, are weakened. Our pre-steady-state kinetic analysis demonstrates that NOD interaction with microtubules occurs slowly with weak activation of ADP product release. Upon rapid substrate binding, NOD detaches from the microtubule prior to the rate-limiting step of ATP hydrolysis, which is also atypical for a kinesin. We propose a model for NOD's microtubule plus-end tracking that drives chromosome movement.


  • Organizational Affiliation

    Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein Nod344Drosophila melanogasterMutation(s): 0 
Gene Names: nodNODACG1763
UniProt
Find proteins for P18105 (Drosophila melanogaster)
Explore P18105 
Go to UniProtKB:  P18105
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18105
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.829α = 90
b = 75.715β = 90
c = 94.58γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
SOLVEphasing
RESOLVEphasing
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations