1YGT | pdb_00001ygt

Dynein Light Chain TcTex-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.235 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1YGT

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of dynein light chain TcTex-1.

Williams, J.C.Xie, H.Hendrickson, W.A.

(2005) J Biological Chem 280: 21981-21986

  • DOI: https://doi.org/10.1074/jbc.M414643200
  • Primary Citation Related Structures: 
    1YGT

  • PubMed Abstract: 

    TcTex-1, one of three dynein light chains of the dynein motor complex, has been implicated in targeting and binding cargoes to cytoplasmic dynein for retrograde or apical transport. Interactions between TcTex-1 and a diverse set of proteins such as the dynein intermediate chain, Fyn, DOC2, FIP1, the poliovirus receptor, CD155, and the rhodopsin cytoplasmic tail have been reported; yet, despite the broad range of targets, a consensus binding sequence remains uncertain. Consequently, we have solved the crystal structure of the full-length Drosophila homolog of TcTex-1 to 1.7 A resolution using MAD phasing to gain insight into its function and target specificity. The structure is homodimeric with a domain swapping of beta-strand 2 and has a fold similar to the dynein light chain, LC8. Based on structural alignment, the TcTex-1 and LC8 sequences show no identity, although the root mean square deviation between secondary structural elements is less than 1.6 A. Moreover, the N terminus, which is equivalent to beta-strand 1 in LC8, is splayed out and binds to a crystallographic dimer as an anti-parallel beta-strand at the same position as the neuronal nitric-oxide synthase peptide in the LC8 complex. Similarity to LC8 and comparison to the LC8-neuronal nitricoxide synthase complex suggest that TcTex-1 binds its targets in a similar manner as LC8 and provides insight to the lack of strict sequence identity among the targets for TcTex-1.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.

Macromolecule Content 

  • Total Structure Weight: 12.59 kDa 
  • Atom Count: 966 
  • Modeled Residue Count: 104 
  • Deposited Residue Count: 111 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytoplasmic dynein light chain111Drosophila melanogasterMutation(s): 0 
Gene Names: Dlc90FTctex
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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.235 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.598α = 90
b = 60.598β = 90
c = 48.485γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
DMphasing
ARP/wARPmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations