4XKK | pdb_00004xkk

Crystal structure of N-terminal domain of Hsp90 from Dictyostelium discoideum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.272 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Heat shock protein 90 regulates development in Dictyostelium discoideum

Sawarkar, R.Roy, N.Rao, S.Raman, S.Venketesh, S.Suguna, K.Tatu, U.

(2008) J Mol Biology 383: 24-35

  • DOI: https://doi.org/10.1016/j.jmb.2008.08.006
  • Primary Citation Related Structures: 
    4XKK

  • PubMed Abstract: 

    Cytosolic heat shock protein 90 (Hsp90) has been implicated in diverse biological processes such as protein folding, cell cycle control, signal transduction, development, and morphological evolution. Model systems available for studying Hsp90 function either allow ease of manipulation for biochemical studies or facilitate a phenomenological study of its role in influencing phenotype. In this work, we have explored the use of the cellular slime mold Dictyostelium discoideum to examine cellular functions of Hsp90 in relation to its multicellular development. In addition to cloning, purification, biochemical characterization, and examination of its crystal structure, our studies, using a pharmacological inhibitor of Hsp90, demonstrate a role for the cytoplasmic isoform (HspD) in D. discoideum development. Inhibition of HspD function using geldanamycin (GA) resulted in delayed aggregation and arrest of D. discoideum development at the 'mound' stage. Crystal structure of the amino-terminal domain of HspD showed a binding pocket similar to that described for yeast Hsp90. Fluorescence spectroscopy, as well as GA-coupled beads affinity pulldown, confirmed a specific interaction between HspD and GA. The results presented here provide an important insight into the function of HspD in D. discoideum development and emphasize the potential of the cellular slime mold to serve as an effective model for studying the many roles of Hsp90 at cellular and organismal levels.


  • Organizational Affiliation
    • Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560 012, India.

Macromolecule Content 

  • Total Structure Weight: 29.23 kDa 
  • Atom Count: 1,700 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 259 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heat shock cognate 90 kDa protein259Dictyostelium discoideumMutation(s): 0 
Gene Names: hspD
UniProt
Find proteins for P54651 (Dictyostelium discoideum)
Explore P54651 
Go to UniProtKB:  P54651
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54651
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.272 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.24α = 90
b = 44.86β = 107.53
c = 60.249γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy