Macromolecule Content

• Total Structure Weight: 14194.79 
• Atom Count: 846 
• Residue Count: 131 
• Unique protein chains: 1

1NYN

Solution NMR Structure of Protein YHR087W from Saccharomyces cerevisiae. Northeast Structural Genomics Consortium Target YTYST425.

• DOI: 10.2210/pdb1NYN/pdb
• BMRB: 5695

• Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-02-13 Released: 2003-04-08 
• Deposition Author(s): Cort, J.R., Yee, A.A., Arrowsmith, C.H., Kennedy, M.A., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 

Literature

The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.

Savchenko, A., Krogan, N., Cort, J.R., Evdokimova, E., Lew, J.M., Yee, A.A., Sanchez-Pulido, L., Andrade, M.A., Bochkarev, A., Watson, J.D., Kennedy, M.A., Greenblatt, J., Hughes, T., Arrowsmith, C.H., Rommens, J.M., Edwards, A.M.

(2005) J.Biol.Chem. 280: 19213-19220

• PubMed: 15701634 
• DOI: 10.1074/jbc.M414421200
• Primary Citation of Related Structures:  
  1P9Q


• PubMed Abstract: 
  

A combination of structural, biochemical, and genetic studies in model organisms was used to infer a cellular role for the human protein (SBDS) responsible for Shwachman-Bodian-Diamond syndrome. The crystal structure of the SBDS homologue in Archaeoglobus fulgidus, AF0491, revealed a three domain protein. The N-terminal domain, which harbors the majority of disease-linked mutations, has a novel three-dimensional fold. The central domain has the common winged helix-turn-helix motif, and the C-terminal domain shares structural homology with known RNA-binding domains. Proteomic analysis of the SBDS sequence homologue in Saccharomyces cerevisiae, YLR022C, revealed an association with over 20 proteins involved in ribosome biosynthesis. NMR structural genomics revealed another yeast protein, YHR087W, to be a structural homologue of the AF0491 N-terminal domain. Sequence analysis confirmed them as distant sequence homologues, therefore related by divergent evolution. Synthetic genetic array analysis of YHR087W revealed genetic interactions with proteins involved in RNA and rRNA processing including Mdm20/Nat3, Nsr1, and Npl3. Our observations, taken together with previous reports, support the conclusion that SBDS and its homologues play a role in RNA metabolism.

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Organizational Affiliation: 

Ontario Center for Structural Proteomics, University of Toronto, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hypothetical 12.0 kDa protein in NAM8-GAR1 intergenic region	A	131	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RTC3
Find proteins for P38804 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38804

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 
• Olderado: 1NYN Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-13 
• Released Date: 2003-04-08 
• Deposition Author(s): Cort, J.R., Yee, A.A., Arrowsmith, C.H., Kennedy, M.A., Northeast Structural Genomics Consortium (NESG)

Revision History 

• Version 1.0: 2003-04-08
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance