3FM7

Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multivalency in the assembly of intrinsically disordered Dynein intermediate chain.

Hall, J.Karplus, P.A.Barbar, E.

(2009) J Biol Chem 284: 33115-33121

  • DOI: https://doi.org/10.1074/jbc.M109.048587
  • Primary Citation of Related Structures:  
    3FM7, 3GLW

  • PubMed Abstract: 

    Dynein light chains are thought to increase binding efficiency of dynein intermediate chain to both dynein heavy chain and dynactin, but their exact role is not clear. Isothermal titration calorimetry and x-ray crystallography reported herein indicate that multivalency effects underlie efficient dynein assembly and regulation. For a ternary complex of a 60-amino acid segment of dynein intermediate chain (IC) bound to two homodimeric dynein light chains Tctex1 and LC8, there is a 50-fold affinity enhancement for the second light chain binding. For a designed IC construct containing two LC8 sites, observed the 1000-fold enhancement reflects a remarkably pure entropic chelate effect of a magnitude commensurate with theoretical predictions. The lower enhancement in wild-type IC is attributed to unfavorable free energy changes associated with incremental interactions of IC with Tctex1. Our results show assembled dynein IC as an elongated, flexible polybivalent duplex, and suggest that polybivalency is an important general mechanism for constructing stable yet reversible and functionally versatile complexes.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain Tctex-type
A, B
111Drosophila melanogasterMutation(s): 0 
Gene Names: Dlc90FTctexCG12363
UniProt
Find proteins for Q94524 (Drosophila melanogaster)
Explore Q94524 
Go to UniProtKB:  Q94524
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94524
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein intermediate chain, cytosolic
C, D
27Drosophila melanogasterMutation(s): 0 
Gene Names: swCdicDic19BCG18000
UniProt
Find proteins for Q24246 (Drosophila melanogaster)
Explore Q24246 
Go to UniProtKB:  Q24246
Entity Groups  
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UniProt GroupQ24246
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmic
E, F
89Drosophila melanogasterMutation(s): 0 
Gene Names: ctpCdlc1ddlc1CG6998
UniProt
Find proteins for Q24117 (Drosophila melanogaster)
Explore Q24117 
Go to UniProtKB:  Q24117
Entity Groups  
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UniProt GroupQ24117
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.180 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.79α = 90
b = 115.79β = 90
c = 90.5γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description