2V66

Crystal Structure of the coiled-coil domain of Ndel1 (a.a. 58 to 169) C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of the Coiled-Coil Domain of Ndel1 and the Basis of its Interaction with Lis1, the Causal Protein of Miller-Dieker Lissencephaly.

Derewenda, U.Tarricone, C.Choi, W.C.Cooper, D.R.Lukasik, S.Perrina, F.Tripathy, A.Kim, M.H.Cafiso, D.S.Musacchio, A.Derewenda, Z.S.

(2007) Structure 15: 1467

  • DOI: 10.1016/j.str.2007.09.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ndel1 and Nde1 are homologous and evolutionarily conserved proteins, with critical roles in cell division, neuronal migration, and other physiological phenomena. These functions are dependent on their interactions with the retrograde microtubule moto ...

    Ndel1 and Nde1 are homologous and evolutionarily conserved proteins, with critical roles in cell division, neuronal migration, and other physiological phenomena. These functions are dependent on their interactions with the retrograde microtubule motor dynein and with its regulator Lis1--a product of the causal gene for isolated lissencephaly sequence (ILS) and Miller-Dieker lissencephaly. The molecular basis of the interactions of Ndel1 and Nde1 with Lis1 is not known. Here, we present a crystallographic study of two fragments of the coiled-coil domain of Ndel1, one of which reveals contiguous high-quality electron density for residues 10-166, the longest such structure reported by X-ray diffraction at high resolution. Together with complementary solution studies, our structures reveal how the Ndel1 coiled coil forms a stable parallel homodimer and suggest mechanisms by which the Lis1-interacting domain can be regulated to maintain a conformation in which two supercoiled alpha helices cooperatively bind to a Lis1 homodimer.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
B, C, D, E
111Homo sapiensMutation(s): 0 
Gene Names: NDEL1 (EOPA, MITAP1, NUDEL)
Find proteins for Q9GZM8 (Homo sapiens)
Go to Gene View: NDEL1
Go to UniProtKB:  Q9GZM8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
B, E
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.431α = 90.00
b = 73.221β = 105.40
c = 69.026γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
SHARPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance