1C03 | pdb_00001c03

CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.248 (Depositor) 
  • R-Value Work: 
    0.206 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1C03

This is version 1.6 of the entry. See complete history

Literature

Insights into eukaryotic multistep phosphorelay signal transduction revealed by the crystal structure of Ypd1p from Saccharomyces cerevisiae.

Song, H.K.Lee, J.Y.Lee, M.G.Moon, J.Min, K.Yang, J.K.Suh, S.W.

(1999) J Mol Biology 293: 753-761

  • DOI: https://doi.org/10.1006/jmbi.1999.3215
  • Primary Citation Related Structures: 
    1C02, 1C03

  • PubMed Abstract: 

    "Two-component" phosphorelay signal transduction systems constitute a potential target for antibacterial and antifungal agents, since they are found exclusively in prokaryotes and lower eukaryotes (yeast, fungi, slime mold, and plants) but not in mammalian organisms. Saccharomyces cerevisiae Ypd1p, a key intermediate in the osmosensing multistep phosphorelay signal transduction, catalyzes the phosphoryl group transfer between response regulators. Its 1.8 A structure, representing the first example of a eukaryotic phosphorelay protein, contains a four-helix bundle as in the HPt domain of Escherichia coli ArcB sensor kinase. However, Ypd1p has a 44-residue insertion between the last two helices of the helix bundle. The side-chain of His64, the site of phosphorylation, protrudes into the solvent. The structural resemblance between Ypd1p and ArcB HPt domain suggests that both prokaryotes and lower eukaryotes utilize the same basic protein fold for phosphorelay signal transduction. This study sheds light on the best characterized eukaryotic phosphorelay system.


  • Organizational Affiliation
    • Department of Chemistry College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.

Macromolecule Content 

  • Total Structure Weight: 77.3 kDa 
  • Atom Count: 5,396 
  • Modeled Residue Count: 652 
  • Deposited Residue Count: 672 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN YDL235C
A, B, C, D
168Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q07688 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07688 
Go to UniProtKB:  Q07688
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07688
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.248 (Depositor) 
  • R-Value Work:  0.206 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.343α = 106.37
b = 66.48β = 106.66
c = 66.491γ = 115.33
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2017-02-08
    Changes: Database references
  • Version 1.5: 2021-07-07
    Changes: Refinement description
  • Version 1.6: 2024-02-07
    Changes: Data collection, Database references