3E2B

Crystal structure of Dynein Light chain LC8 in complex with a peptide derived from Swallow


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8.

Benison, G.Karplus, P.A.Barbar, E.

(2008) J.Mol.Biol. 384: 954-966

  • DOI: 10.1016/j.jmb.2008.09.083
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes unrelated to molecular motors. ...

    Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes unrelated to molecular motors. LC8 binds to two families of targets: those having a KXTQT sequence fingerprint and those having a GIQVD fingerprint. All known LC8 binding partners containing these fingerprints share a common binding site on LC8 that raises the question of what determines binding specificity. Here, we present the crystal structure of apo-LC8 at 1.7-A resolution, which, when compared with the crystal structures of several LC8 complexes, gives insight into the mechanism underlying the binding diversity of LC8. Peptide binding is associated with a shift in quaternary structure that expands the hydrophobic binding surface available to the ligand, in addition to changes in tertiary structure and ordering of LC8 around the binding groove. The observed quaternary shift suggests a mechanism by which binding at one of the two identical sites can influence binding at the other. NMR spectra of titrations with peptides from each fingerprint family show evidence of allosteric interaction between the two binding sites, to a differing degree in the two ligand families. Allosteric interaction between the binding sites may be a mechanism to promote simultaneous binding of ligands from the same family, providing a physiological role for the two fingerprints.


    Related Citations: 
    • Structure and dynamics of LC8 complexes with KXTQT-motif peptides: swallow and dynein intermediate chain compete for a common site.
      Benison, G.,Karplus, P.A.,Barbar, E.
      (2007) J.Mol.Biol. 371: 457


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynein light chain 1, cytoplasmic
A
89Drosophila melanogasterMutation(s): 0 
Gene Names: ctp (Cdlc1, ddlc1)
Find proteins for Q24117 (Drosophila melanogaster)
Go to UniProtKB:  Q24117
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein swallow 16-residue peptide
C
16Drosophila melanogasterMutation(s): 0 
Gene Names: swa
Find proteins for P40688 (Drosophila melanogaster)
Go to UniProtKB:  P40688
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.158α = 90.00
b = 44.158β = 90.00
c = 203.718γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance