2HZ5

Crystal structure of human dynein light chain Dnlc2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human dynein light chain Dnlc2A: Structural insights into the interaction with IC74

Liu, J.-F.Wang, Z.-X.Wang, X.-Q.Tang, Q.An, X.-M.Gui, L.-L.Liang, D.-C.

(2006) Biochem.Biophys.Res.Commun. 349: 1125-1129

  • DOI: 10.1016/j.bbrc.2006.08.161

  • PubMed Abstract: 
  • The human light chain of the motor protein dynein, Dnlc2A, is also a novel TGF-beta-signaling component, which is altered with high frequency in epithelial ovarian cancer. It is an important mediator of dynein and the development of cancer, owing to ...

    The human light chain of the motor protein dynein, Dnlc2A, is also a novel TGF-beta-signaling component, which is altered with high frequency in epithelial ovarian cancer. It is an important mediator of dynein and the development of cancer, owing to its ability to bind to the dynein intermediate light chain (DIC) IC74 and to regulate TGF-beta-dependent transcriptional events. Here we report the 2.1-A crystal structure of Dnlc2A using single anomalous diffraction. The proteins form a homodimer in solution and interact mainly through the helix alpha(2), strand beta(3), and the loop following this strand in each protein to generate a 10-stranded beta-sheet core. The surface of the beta-sheet core is mainly positively charged and predicted (by software PPI-Pred) to be the site that interacts with other partners. At the same time, the residues 79-82, 88, and 90 of each molecule formed two holes in the core. Residue 89 of each molecule, which is crucial for the DIC binding function of Dnlc2A, is within the holes. On the basis of these observations, we propose that the homodimer is the structural and functional unit maintained by hydrogen bonding interactions and hydrophobic packing, and that the patch of the surface of the beta-sheet core is the main area of interaction with other partners. Furthermore, the two holes would be the key sites to interact with IC74.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynein light chain 2A, cytoplasmic
A, B
106Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1 (BITH, DNCL2A, DNLC2A, ROBLD1)
Find proteins for Q9NP97 (Homo sapiens)
Go to Gene View: DYNLRB1
Go to UniProtKB:  Q9NP97
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CS
Query on CS

Download SDF File 
Download CCD File 
B
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 83.150α = 90.00
b = 83.150β = 90.00
c = 98.128γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance