3RBY | pdb_00003rby

Crystal structure of uncharacterized protein YLR301w from Saccharomycces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3RBY/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.247 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

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

• PubMed: 22525751 
• DOI: https://doi.org/10.1107/S090744491200491X
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.36 kDa 
• Atom Count: 4,127 
• Modeled Residue Count: 490 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YLR301W	A, B	245	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YLR301W
UniProt
Find proteins for Q05905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05905  Go to UniProtKB:  Q05905

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.247 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.32	α = 90
b = 122.32	β = 90
c = 174.001	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations