3GLW | pdb_00003glw

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

• PDB DOI: https://doi.org/10.2210/pdb3GLW/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-12 Released: 2009-09-15 
• Deposition Author(s): Hall, J.D., Karplus, P.A., Barbar, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.271 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Multivalency in the assembly of intrinsically disordered Dynein intermediate chain.

Hall, J., Karplus, P.A., Barbar, E.

(2009) J Biological Chem 284: 33115-33121

• PubMed: 19759397 
• DOI: https://doi.org/10.1074/jbc.M109.048587
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.59 kDa 
• Atom Count: 870 
• Modeled Residue Count: 103 
• Deposited Residue Count: 117 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain 1, cytoplasmic	A	89	Drosophila melanogaster	Mutation(s): 0  Gene Names: ctp, Cdlc1, ddlc1, CG6998
UniProt
Find proteins for Q24117 (Drosophila melanogaster) Explore Q24117  Go to UniProtKB:  Q24117

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein intermediate Chain	B [auth Z]	28	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.271 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.645	α = 90
b = 44.645	β = 90
c = 219.376	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Hall, J.D., Karplus, P.A., Barbar, E.J.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary