3K6T | pdb_00003k6t

Crystal structure of the GLD-1 homodimerization domain from Caenorhabditis elegans at 2.04 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3K6T

This is version 1.3 of the entry. See complete history

Literature

Structure of the GLD-1 homodimerization domain: insights into STAR protein-mediated translational regulation.

Beuck, C.Szymczyna, B.R.Kerkow, D.E.Carmel, A.B.Columbus, L.Stanfield, R.L.Williamson, J.R.

(2010) Structure 18: 377-389

  • DOI: https://doi.org/10.1016/j.str.2009.12.016
  • Primary Citation Related Structures: 
    3K6T, 3KBL

  • PubMed Abstract: 

    Posttranscriptional regulation of gene expression is an important mechanism for modulating protein levels in eukaryotes, especially in developmental pathways. The highly conserved homodimeric STAR/GSG proteins play a key role in regulating translation by binding bipartite consensus sequences in the untranslated regions of target mRNAs, but the exact mechanism remains unknown. Structures of STAR protein RNA binding subdomains have been determined, but structural information is lacking for the homodimerization subdomain. Here, we present the structure of the C. elegans GLD-1 homodimerization domain dimer, determined by a combination of X-ray crystallography and NMR spectroscopy, revealing a helix-turn-helix monomeric fold with the two protomers stacked perpendicularly. Structure-based mutagenesis demonstrates that the dimer interface is not easily disrupted, but the structural integrity of the monomer is crucial for GLD-1 dimerization. Finally, an improved model for STAR-mediated translational regulation of mRNA, based on the GLD-1 homodimerization domain structure, is presented.


  • Organizational Affiliation
    • Department of Molecular Biology, Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 27.55 kDa 
  • Atom Count: 1,788 
  • Modeled Residue Count: 203 
  • Deposited Residue Count: 240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Female germline-specific tumor suppressor gld-1
A, B, C, D
60Caenorhabditis elegansMutation(s): 0 
Gene Names: gld-1T23G11.3
UniProt
Find proteins for Q17339 (Caenorhabditis elegans)
Explore Q17339 
Go to UniProtKB:  Q17339
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ17339
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.889α = 90
b = 42.962β = 90
c = 154.641γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Advisory, Data collection, Database references