1OXK

Complex between YPD1 and SLN1 response regulator domain in space group P3(2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Yeast YPD1/SLN1 Complex. Insights into Molecular Recognition in Two-Component Signaling Systems.

Xu, Q.Porter, S.W.West, A.H.

(2003) Structure 11: 1569-1581

  • DOI: 10.1016/j.str.2003.10.016
  • Primary Citation of Related Structures:  
    1OXB, 1OXK

  • PubMed Abstract: 
  • In Saccharomyces cerevisiae, a branched multistep phosphorelay signaling pathway regulates cellular adaptation to hyperosmotic stress. YPD1 functions as a histidine-phosphorylated protein intermediate required for phosphoryl group transfer from a membrane-bound sensor histidine kinase (SLN1) to two distinct response regulator proteins (SSK1 and SKN7) ...

    In Saccharomyces cerevisiae, a branched multistep phosphorelay signaling pathway regulates cellular adaptation to hyperosmotic stress. YPD1 functions as a histidine-phosphorylated protein intermediate required for phosphoryl group transfer from a membrane-bound sensor histidine kinase (SLN1) to two distinct response regulator proteins (SSK1 and SKN7). These four proteins are evolutionarily related to the well-characterized "two-component" regulatory proteins from bacteria. Although structural information is available for many two-component signaling proteins, there are very few examples of complexes between interacting phosphorelay partners. Here we report the first crystal structure of a prototypical monomeric histidine-containing phosphotransfer (HPt) protein YPD1 in complex with its upstream phosphodonor, the response regulator domain associated with SLN1.


    Related Citations: 
    • Co-Crystallization of the Yeast Phosphorelay Protein YPD1 with the SLN1 Response-Regulator Domain and Preliminary X-ray Diffraction Analysis
      Chooback, L., West, A.H.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 927

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ypd1p
A, C, E, G, I, K
A, C, E, G, I, K
166Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YPD1
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SLN1
B, D, F, H, J, L
B, D, F, H, J, L
134Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLN1 OR YPD2 OR YIL147C
EC: 2.7.3 (PDB Primary Data), 2.7.13.3 (UniProt)
UniProt
Find proteins for P39928 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39928 
Go to UniProtKB:  P39928
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39928
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth J],
BA [auth K],
CA [auth K],
DA [auth L],
M [auth A],
AA [auth J],
BA [auth K],
CA [auth K],
DA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth E],
T [auth E],
U [auth F],
V [auth G],
W [auth G],
X [auth H],
Y [auth I],
Z [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.3α = 90
b = 91.3β = 90
c = 200.35γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance