5E0M

LC8 - Chica (468-476) Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Anchored Flexibility Model in LC8 Motif Recognition: Insights from the Chica Complex.

Clark, S.Nyarko, A.Lohr, F.Karplus, P.A.Barbar, E.

(2016) Biochemistry 55: 199-209

  • DOI: 10.1021/acs.biochem.5b01099
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LC8 is a dimeric hub protein involved in a large number of interactions central to cell function. It binds short linear motifs--usually containing a Thr-Gln-Thr (TQT) triplet--in intrinsically disordered regions of its binding partners, some of which ...

    LC8 is a dimeric hub protein involved in a large number of interactions central to cell function. It binds short linear motifs--usually containing a Thr-Gln-Thr (TQT) triplet--in intrinsically disordered regions of its binding partners, some of which have several LC8 recognition motifs in tandem. Hallmarks of the 7-10 amino acid motif are a high variability of LC8 binding affinity and extensive sequence permutation outside the TQT triplet. To elucidate the molecular basis of motif recognition, we use a 69-residue segment of the human Chica spindle adaptor protein that contains four putative TQT recognition motifs in tandem. NMR-derived secondary chemical shifts and relaxation properties show that the Chica LC8 binding domain is essentially disordered with a dynamically restricted segment in one linker between motifs. Calorimetry of LC8 binding to synthetic motif-mimicking peptides shows that the first motif dominates LC8 recruitment. Crystal structures of the complexes of LC8 bound to each of two motif peptides show highly ordered and invariant TQT-LC8 interactions and more flexible and conformationally variable non-TQT-LC8 interactions. These data highlight rigidity in both LC8 residues that bind TQT and in the TQT portion of the motif as an important new characteristic of LC8 recognition. On the basis of these data and others in the literature, we propose that LC8 recognition is based on rigidly fixed interactions between LC8 and TQT residues that act as an anchor, coupled with inherently flexible interactions between LC8 and non-TQT residues. The "anchored flexibility" model explains the requirement for the TQT triplet and the ability of LC8 to accommodate a large variety of motif sequences and affinities.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States.




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 Chica peptide
C
13Homo sapiensMutation(s): 0 
Gene Names: FAM83D (C20orf129)
Find proteins for Q9H4H8 (Homo sapiens)
Go to Gene View: FAM83D
Go to UniProtKB:  Q9H4H8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.207 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.540α = 90.00
b = 44.540β = 90.00
c = 205.016γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHENIXphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description