1P9Q

Structure of a hypothetical protein AF0491 from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M414421200
  • Primary Citation of Related Structures:  1NYN

  • 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 Archaeog ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein AF0491
C
256Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)N/A
Find proteins for O29759 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O29759
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.219 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.875α = 92.74
b = 44.254β = 118.02
c = 61.418γ = 109.67
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
SnBphasing
CNSrefinement
SCALEPACKdata scaling
ARP/wARPmodel building
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-02-14
    Type: Experimental preparation