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

Experimental Data Snapshot

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

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This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1074/jbc.M414421200
  • Primary Citation of Related Structures:  
    1NYN, 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical 12.0 kDa protein in NAM8-GAR1 intergenic region131Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YHR087W
Find proteins for P38804 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38804 
Go to UniProtKB:  P38804
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38804
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection