3RBY

Crystal structure of uncharacterized protein YLR301w from Saccharomycces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel beta-structure of YLR301w from Saccharomyces cerevisiae.

Kim, K.H.Ahn, H.J.Lee, W.K.Lee, C.Yu, M.H.Kim, E.E.

(2012) Acta Crystallogr D Biol Crystallogr 68: 531-540

  • DOI: 10.1107/S090744491200491X
  • Primary Citation of Related Structures:  
    3RBY

  • PubMed Abstract: 
  • When the Z-type variant of human α(1)-antitrypsin was overexpressed in Saccharomyces cerevisiae, proteomics analysis identified YLR301w as one of the up-regulated proteins. YLR301w is a 27.5 kDa protein with no sequence homology to any known protein and has been reported to interact with Sec72 and Hrr25 ...

    When the Z-type variant of human α(1)-antitrypsin was overexpressed in Saccharomyces cerevisiae, proteomics analysis identified YLR301w as one of the up-regulated proteins. YLR301w is a 27.5 kDa protein with no sequence homology to any known protein and has been reported to interact with Sec72 and Hrr25. The crystal structure of S. cerevisiae YLR301w has been determined at 2.3 Å resolution, revealing a novel β-structure. It consists of an N-terminal ten-stranded β-barrel with two short α-helices connected by a 23-residue linker to a seven-stranded half-barrel with two short helices at the C-terminus. The N-terminal barrel has a highly conserved hydrophobic channel that can bind hydrophobic molecules such as PEG. It forms a homodimer both in the crystal and in solution. YLR301w binds Sec72 with a K(d) of 6.2 µM, but the biological significance of this binding requires further investigation.


    Organizational Affiliation

    Biomedical Research Institute, Korea Institute of Science and Technology, 39-1 Hawolkok-dong, Sungbuk-gu, Seoul 136-791, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YLR301WA, B245Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YLR301W
UniProt
Find proteins for Q05905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05905 
Go to UniProtKB:  Q05905
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.32α = 90
b = 122.32β = 90
c = 174.001γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2011-03-30 
  • Released Date: 2012-03-21 
  • Deposition Author(s): Kim, K.-H., Kim, E.E.

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references