JCSG News and Highlights

Hot off the press

JCSG Special Issue of Acta Crystallographica Section F: In an effort to increase the visibility and impact of our structures, as well as highlight Acta F as a suitable forum to foster communication of such structural genomics structures, the JCSG was invited by the journal editors to do a special “JCSG only” issue of Acta Crystallographica Section F: Structural Biology and Crystallization Communications (Acta F). We have recently completed this JCSG Issue of Acta F (Volume 66 Part 10) that focuses on 6 areas of research that are directly impacted by our work and highlights specific sets of structures, as well as HT technologies and communication tools that were developed at the JCSG. This issue of Acta F is subdivided into sections where external experts have written stimulating overviews that provide independent analysis and context for the specific topics and groups of JCSG papers. These sections are:

  • JCSG pipeline: technology and dissemination
  • Domains of unknown function - Commentary by A. Bateman, P. Coggill and R. D. Finn
  • New folds - Commentary by A. Andreeva and A. G. Murzin
  • Novel variants of know fold and function - Commentary by E. V. Koonin
  • Human gut microbiome - Commentary by P. J. Turnbaugh, B. Henrissat and J. I. Gordon
  • Ligands that aid in function characterization - Commentary by A. E. Speers and B. F. Cravatt
  • NMR in a high-throughput NMR in a HT environment - Commentary by K. Wüthrich

This issue is Open Access and is available online as of Sept 30, 2010
(http://journals.iucr.org/f/issues/2010/10/00/isscontsbdy.html ).

 

 

Recent Press

Scripps Research Scientists Win $65 Million in New Grants
http://www.scripps.edu/newsandviews/i_20101004/grants.html

NIH Grants Will Advance Studies of the Form and Function of Proteins
http://www.nigms.nih.gov/News/Results/20100930.htm

 

 

News and Highlights

The JCSG Deposits 1000th Structure in the PDB: We are pleased to announce that on March 1st, 2010, the JCSG deposited its 1000th structure in the Protein Data Base. This amazing feat would never have been possible without the hard work and dedication from each and every member of our great JCSG team. Congratulations to everyone! To put this in perspective, recall that at the onset of PSI-2, we started off with approximately 200 structures in the PDB.

JCSG Website Updated: In an effort to modernize and improve our public image, the new JCSG website (www.jcsg.org) went online on March 19th. Many thanks to everybody involved, in particular Andrew Morse and Marc Elsliger. New features will be added to the site in the next month to facilitate interaction with collaborators and PSI:Biology partner centers.

 

 

PSI:Biology Materials Repository

The JCSG Thermatoma Maritima collection was the first “PSI Plasmid of the Month” featured on the PSI-MR website http://dnasu.asu.edu/DNASU/POMApril10.jsp.

 

 

PSI Structural Biology Knowledgebase | Nature Gateway Highlights

The JCSG worked closely with Nature editors and the Knowledgebase in editing 22 articles highlighting the achievements of PSI-2, which were released in the July-October 2010 web releases.
(http://kb.psi-structuralgenomics.org/update/2010/09/research.html).

 

 

PSI Structural Biology Knowledgebase | Nature Gateway Featured Articles      

April 2010, “Bacterial Spore Kinase.” 
http://kb.psi-structuralgenomics.org/update/2010/04/full/fa_psisgkb.2010.12.html
E. D. Scheef et al. Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. Proteins, 78: 1470-1482 (2009).

January 2010, “First bacterial PH domain.”
http://kb.psi-structuralgenomics.org/update/2010/01/full/fa_psisgkb.2009.59.html
Q. Xu et al. Bacterial Pleckstrin homology domains: A prokaryotic origin for the PH domain. J Mol Biol., 396: 31-46 (2010).

December 2009, “What have we learned from domains of unknown function?”
http://kb.psi-structuralgenomics.org/update/2009/12/full/fa_psisgkb.2009.54.html  
L. Jaroszewski et al. Exploration of uncharted regions of the protein universe. PLoS Biol., 7:e1000205 (2009).

November 2009, “Network coverage.” 
http://kb.psi-structuralgenomics.org/update/2009/11/full/fa_psisgkb.2009.48.html
Y. Zhang et al.  Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325: 1544-1549 (2009).

October 2009, “Unusual cell division”.
http://kb.psi-structuralgenomics.org/update/2009/10/full/fa_psisgkb.2009.43.html
Q. Xu et al. Structural and functional characterization of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes. J. Biol. Chem., 284: 25268-25279 (2009).

April 2009, “Unique SARS”.
http://kb.psi-structuralgenomics.org/update/2009/04/full/fa_psisgkb.2009.12.html
A. Chatterjee et al. Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. J. Virol., 83: 1823-1836 (2009).   PMCID: PMC2643772  

September 2008, “SARS connections”.
http://kb.psi-structuralgenomics.org/update/2008/09/full/fa_psisgkb.2008.3.html
B.W. Newman et al. Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3. J Virol., 82: 5279-5294 (2008).

 

 

PSI Structural Biology Knowledgebase | Nature Gateway Featured Technical highlights

January 2009, “Speeding cloning and mutagenesis”.
http://kb.psi-structuralgenomics.org/update/2009/01/full/th_psisgkb.2008.24.html
H.E. Klock et al. Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins, 71: 982-994 (2008).

February 2009, “Dealing with difficult families”.
http://kb.psi-structuralgenomics.org/update/2009/02/full/th_psisgkb.2009.2.html
L. Jaroszewski et al. Genome pool strategy for structural coverage of protein families. Structure, 16: 1659-1667 (2008).

 

 

PSI Structural Biology Knowledgebase | Nature Gateway Featured Structures

October 2010, “Alpha/Beta Barrels”.
http://kb.psi-structuralgenomics.org/KB/index1.jsp?pageshow=72   
Y. Zhang et al.  Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325: 1544-1549 (2009).

May 2010, “Mre11 Nuclease.”
http://kb.psi-structuralgenomics.org/KB/archives.jsp?pageshow=26
D. Das et al. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol., 397: 647-663.

April 2009, “Hda and DNA Replication”.
http://kb.psi-structuralgenomics.org/KB/archives.jsp?pageshow=15
References included: Q. Xu et al. A structural basis for the regulatory inactivation of DnaA.  J. Mol. Biol., 385: 368-380 (2009).

2008, “Scavenger Decapping Enzyme DCps”.
http://kb.psi-structuralgenomics.org/KB/archives.jsp?pageshow=9   
References included: G.W. Ha, et al. Crystal Structure of an Apo mRNA Decapping Enzyme (DcpS) from Mouse at 1.83 Å Resolution. Proteins, 60: 797-802 (2005).

2008, “SARS Coronavirus Nonstructural Protein 1”.
http://kb.psi-structuralgenomics.org/KB/archives.jsp?pageshow=4   
References included: M.S. Almeida et al. Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from severe acute respiratory syndrome coronavirus. J Virol,, 81: 3151-3161 (2007).

2008, “Glycerate Kinase”.
http://kb.psi-structuralgenomics.org/KB/archives.jsp?pageshow=1
References included: R. Schwarzenbacker, et al. Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold. Proteins, 65: 243-248 (2006).