Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.72 kDa 
• Atom Count: 1904 
• Modelled Residue Count: 230 
• Deposited Residue Count: 240 
• Unique protein chains: 1

1T95

Crystal Structure of the Shwachman-Bodian-Diamond Syndrome Protein Orthologue from Archaeoglobus fulgidus

• PDB DOI: 10.2210/pdb1T95/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-14 Released: 2004-06-22 
• Deposition Author(s): Shammas, C., Warren, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Structural and mutational analysis of the SBDS protein family. Insight into the leukemia-associated Shwachman-Diamond Syndrome.

Shammas, C., Menne, T.F., Hilcenko, C., Michell, S.R., Goyenechea, B., Boocock, G.R., Durie, P.R., Rommens, J.M., Warren, A.J.

(2005) J Biol Chem 280: 19221-19229

• PubMed: 15701631 
• DOI: 10.1074/jbc.M414656200
• Primary Citation of Related Structures:  
  1T95


• PubMed Abstract: 
  

Shwachman-Diamond Syndrome (SDS) is an autosomal recessive disorder characterized by bone marrow failure with significant predisposition to the development of poor prognosis myelodysplasia and leukemia, exocrine pancreatic failure and metaphyseal chondrodysplasia. Although the SBDS gene mutated in this disorder is highly conserved in Archaea and all eukaryotes, the function is unknown. To interpret the molecular consequences of SDS-associated mutations, we have solved the crystal structure of the Archaeoglobus fulgidus SBDS protein orthologue at a resolution of 1.9 angstroms, revealing a three domain architecture. The N-terminal (FYSH) domain is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold identical to the single domain yeast protein Yhr087wp that is implicated in RNA metabolism. The central domain consists of a three-helical bundle, whereas the C-terminal domain has a ferredoxin-like fold. By genetic complementation analysis of the essential Saccharomyces cerevisiae SBDS orthologue YLR022C, we demonstrate an essential role in vivo for the FYSH domain and the central three-helical bundle. We further show that the common SDS-related K62X truncation is non-functional. Most SDS-related missense mutations that alter surface epitopes do not impair YLR022C function, but mutations affecting residues buried in the hydrophobic core of the FYSH domain severely impair or abrogate complementation. These data are consistent with absence of homozygosity for the common K62X truncation mutation in individuals with SDS, indicating that the SDS disease phenotype is a consequence of expression of hypomorphic SBDS alleles and that complete loss of SBDS function is likely to be lethal.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein AF0491	A	240	Archaeoglobus fulgidus	Mutation(s): 5  Gene Names: AF0491
UniProt
Find proteins for O29759 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29759  Go to UniProtKB:  O29759

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.668	α = 75.87
b = 44.448	β = 85.61
c = 54.72	γ = 69.49

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-14 
• Released Date: 2004-06-22 
Deposition Author(s): Shammas, C., Warren, A.J.

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance