Dear Consortium Members and Affiliates,
We're slipping our November newsletter out before the Thanksgiving holiday brings things to a halt here in the U.S. SBGrid will be closed November 27-28th and, while we'll be keeping an eye on things, we'll only attend to the big stuff between now and December 1st. Until then, please read below for a link to last week's webinar recording, a Support Forum tip on controlling software versions, a story on Pedro Pereira from Portugal, several software updates, software version freezes, and one new SBGrid member. Happy Thanksgiving to all who celebrate!
In last week's webinar Tom Grant gave Part II of his SAXS presentation, which is now available on our YouTube channel. We'll be taking a break for the month of December, but will hear about SPARX from Pawel Penczek on January 20th. Be sure to join us!
From the SBGrid Support Forums we're highlighting an article on version control. SBGrid regularly pushes out software updates and sometimes the newest versions bring unexpected bugs. For this or any other reason you can quickly switch to an older version of an application. Using CCP4 as an example:
- The default version of CCP4 on Linux is 6.4, but versions 6.3 and 6.2 are also available. To see a list of all available versions run: sbgrid -l ccp4.
- to change your default version to 6.2 on Linux you'll need to add the following line to the '.sbgrid.conf' file in your home directory: CCP4_X=6.2.
Our November Tale includes a theme to whet the appetite, more apropos of Halloween than Thanksgiving: leeches. Pedro Pereira, Group Leader at the Institute for Molecular and Cell Biology in Porto Portugal, explains how the leeches that were studied in his graduate mentor's lab provided the fuel for much of his future research.
On the software front, with new versions of Mac and Linux and growing compatibility problems running older operating systems and architectures, we're freezing software updates for Cent OS5, Mac OS X 10.6, and the Linux 32-bit software tree. We will continue to support the existing software collection for these operating systems/architecture, but as of January 1, 2015, no updates or new software titles will be added.
As for software updates, this month we have new versions of CTF, Phenix, Ringer, and XDS along with the addition of one new software application: Scatter.
November saw one new member join SBGrid: Peng Gong from the Wuhan Branch of the Chinese Academy of Science. Welcome Peng Gong!
CTF was updated to version 20140609 and we have another update in the queue (CTFfind4) that will bring this software up to the latest version.
The Phenix nightly build dev-1839 was pushed out.
Ringer was updated to version 2.0.
We've added Scatter to the SBGrid software collection, courtesy of Robert Rambo of Diamond Light Source. Scatter is an application for basic analysis of SAXS datasets.
XDS was updated to version 20141103 and now accepts XZ-compressed image files and images obtained by the EIGER detector.
Included below is a selection of publications that have appeared from Consortium member laboratories over the past 30 days. For the full list of publications please visit the Member Publications page on the SBGrid website.
- Ning Zheng's Group, U Washington: Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module.
- Dinshaw Patel's Group, Memorial Sloan-Kettering Cancer Center: In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.
- Joseph Piccirilli's Group, U Chicago: Origins of life: RNA made in its own mirror image.
- Christopher Lima's Group, Memorial Sloan-Kettering Institute: Fission yeast RNA triphosphatase reads an Spt5 CTD code.
- Bill Weis's Group, Stanford U: Mechano-Transduction: From Molecules to Tissues.
- Mark Mayer's Group, NIH: Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports.
- Jane McGlade's Group, U Toronto: Comprehensive Identification of Phosphorylation Sites on theNumb Endocytic Adaptor Protein.
- Gerhard Wagner's Group, Harvard Medical School: G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments.
- Tom Rapoport's Group, Harvard Medical School: A model for the generation and interconversion of ER morphologies.
- Suzanne Walker's Group, Harvard Medical School: Lipid-linked cell wall precursors regulate membrane association of bacterial actin MreB.
- Demetrios Braddock's Group, Yale U: MicroRNA silencing for cancer therapy targeted to the tumour microenvironment.
- Marc Kvansakul's Group, La Trobe U: The Bcl-2 family: structures, interactions and targets for drug discovery.
- James Bradner's Group, Dana-Farber Cancer Institute: Structure-Guided DOT1L Probe Optimization by Label-Free Ligand < Displacement.
- Andrew Wang's Group, Academia Sinica: Pin1-mediated Sp1 phosphorylation by CDK1 increases Sp1 stability and decreases its DNA-binding activity during mitosis.
- Andreas Plückthun's Group, U Zurich: Novel Prodrug-Like Fusion Toxin with Protease-Sensitive Bioorthogonal PEGylation for Tumor Targeting.
- Raimond Dutzler's Group, U Zurich: X-ray structure of a calcium-activated TMEM16 lipid scramblase.
- Jens Meiler's Group, Vanderbilt U: Analysis of Nidogen-1/Laminin γ1 Interaction by Cross-Linking, Mass Spectrometry, and Computational Modeling Reveals Multiple Binding Modes.
- Teru Nakagawa's Group, Vanderbilt U: Structural basis for extracellular cis and trans RPTPσ signal competition in synaptogenesis.
- John Markley's Group, U Wisconsin-Madison: The Specialized Hsp70 (HscA) Interdomain Linker Binds to Its Nucleotide-Binding Domain and Stimulates ATP Hydrolysis in Both cis and trans Configurations.
- Steve Fesik's Group, Vanderbilt: Fragment-Based Screening of the Bromodomain of ATAD2.
- Pamela Bjorkman's Group, Caltech: Enhanced HIV-1 immunotherapy by commonly arising antibodies that target virus escape variants.
- Tim Springer's Group, Boston Children's Hospital: Structural determinants of integrin β-subunit specificity for latent TGF-β
- Tom Walz's Group, Harvard Medical School: Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase.
- Luke Rice's Group, U Texas Southwestern: The contribution of αβ-tubulin curvature to microtubule dynamics.
- Rachelle Gaudet's Group, Harvard U: Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter.
- Andres Leschziner's Group, Harvard U: Lis1 regulates dynein by sterically blocking its mechanochemical cycle.
- Ivan Rayment's Group, U Wisconsin-Madison: Insights Into the Specificity of Lysine Acetyltransferases.
- James Hogel's Group, Harvard Medical School: Structural Dynamics as a Contributor to Error-prone Replication by a RNA-dependent RNA Polymerase.
- Axel Brunger, Stanford U: Direct Visualization of Trans-Synaptic Neurexin-Neuroligin Interactions during Synapse Formation.
- Enrico DiCera's Group, St. Louis U: WEDGE: An anticoagulant thrombin mutant produced by autoactivation.
- Steven Blacklow's Group, Harvard Medical School: Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia.
- Michael Sattler, Institute of Structural Biology, Germany: Artificial accelerators of the molecular chaperone hsp90 facilitate rate-limiting conformational transitions.
- Jamie Cate's Group, U California Berkeley: Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.
- Cynthia Wolberger's Group, Johns Hopkins U School of Medicine: Extracellular nicotinamide phosphoribosyltransferase (NAMPT) promotes M2 macrophage polarization in chronic lymphocytic leukemia.
- Phillipp Selenko's Group, Leibniz Institute of Molecular Pharmacology: Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells.
- Peter Kwong's Group, NIH:
- Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo.
- Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.
Please cite eLife 2013;2:e01456 for all projects completed with SBGrid compiled software.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.