[ccp4bb] PhD (CIFRE) position – SANOFI & ESRF on cryoEM methods applied to antibodies
PhD (CIFRE) position – SANOFI & ESRF on cryoEM methods applied to antibodies PhD thesis title: High resolution Cryo- Electron Microscopy of Antibody / Antigen complexes More and more research focus is being put on biologics and their development as drugs. These molecules are usually large and flexible and they can interact with various targets located on the surface of cells; Bi-specific antibodies are an example that can potentially bind to two different antigens and which have gained attention due to their potential application in cancer immunotherapy and drug delivery. To fully understand their mechanism, structural knowledge at an atomic level is needed. While low resolution studies can be obtained using traditional microscopy, high resolution studies of these interactions are usually performed by protein crystallography (or by Hydrogen Deuterium Exchange studies) using fragments of both antibody and antigen. The ESRF is in progress of installing a Krios microscope which, coupled with a direct electron detector and a Volta phase plate will enable us to determine the full structure of the complexes. The successful candidate will characterise Ag/Biologics complexes from Sanofi, using state-of-the-art microscopes at the cryo-EM platform of the Partnership for Structural Biology (PSB) and will determine the high-resolution structure of one or more of these complexes. The PhD thesis will last 3 years starting in late autumn 2017, in a collaboration between Sanofi (Vitry sur Seine, France) and the ESRF (Grenoble, France) under the co-supervision of Dr. Magali Mathieu (Sanofi) and Dr. Gordon Leonard (ESRF). This thesis will be CIFRE (Conventions Industrielles de Formation par la REcherche) and the student will be a Sanofi employee (CDD) for the whole duration of the thesis. Most of his/her work will be performed at the ESRF. The applicant must have a Master Degree (Master2 or MSc) in integrated structural biology or biophysics, some knowledge in cryo-electron microscopy and in molecular and cell biology. He/she should be a team player and have good communication skills. CV and accompanying letter should be sent to magali.math...@sanofi.com<mailto:magali.math...@sanofi.com> AND christoph.mueller_dieckm...@esrf.fr<mailto:christoph.mueller_dieckm...@esrf.fr> before July 7, 2017. Magali Mathieu Sanofi Bio Structure and Biophysics / iDD France Centre de Recherche de Vitry/Alfortville TÉL. : +33 (0) 1.58.93.39.90 - FAX : +33 (0) 1.58.93.80.63 13, quai Jules Guesde – BP 14 – 94403 Vitry-sur-Seine Cedex France [cid:image001.jpg@01D28B97.134FDFD0]
[ccp4bb] TR: [ccp4bb] KRAS maps
Hi Nick, Robbie, I encountered the same problem. This is not a bug but the way the data was deposited. They have deposited intensities. What I did to be able to look at the maps: Retrieve the structure factor file, which in fact contains intensities Run it through Truncate to get Fs Remove the ligand from the PDB REFMAC still refused to read in the new mtz file, for a reason I could not find. But BUSTER took it without problem Then look at the electron density in COOT... if the ligand was properly present, it should come clearly in the difference density Magali Mathieu Head of SB-X2S Sanofi LGCR - SDI Centre de Recherche de Vitry/Alfortville TÉL. : +33 (0) 1.58.93.39.90 - FAX : +33 (0) 1.58.93.80.63 13, quai Jules Guesde – BP 14 – 94403 Vitry-sur-Seine Cedex France Please consider the environment before printing this email! -Message d'origine- De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Robbie Joosten Envoyé : vendredi 29 août 2014 15:48 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] KRAS maps Hi Nick, Not sure what happened here, it seems like a bug in this EDS entry. You can try PDB_REDO for maps. In recent versions of COOT (version 0.8*) the button for getting maps and a model is just under that for EDS. There is a plugin for older versions of COOT. They look okay, but the model has changed (on purpose). If you prefer looking at maps for an unmodified model you can download the mtz files here: http://www.cmbi.ru.nl/pdb_redo/lu/4luc/4luc_0cyc.mtz.gz http://www.cmbi.ru.nl/pdb_redo/lv/4lv6/4lv6_0cyc.mtz.gz Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nicholas Larsen Sent: Friday, August 29, 2014 15:36 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] KRAS maps Dear All, I frequently use the Coot feature Fetch PDB and MAP using EDS... with great success when peer reviewing literature reports. However, when I try this for the recent KRAS structures deposited by Kevan Shokat and Jim Wells (Nature 2013), the Coot generated maps are garbage, although the resolution is better than 1.5 A. Does anyone have an explanation? I also checked with one kind colleague at another institute and she confirmed my problem using Linux platform (I am using Windows). See PDBs, 4LUC and 4LV6, for example. Cheers, Nick [This e-mail message may contain privileged, confidential and/or proprietary information of H3 Biomedicine. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.]
[ccp4bb] problem with installation of Balbes 1.0.0
Hello all, following the latest workshop, we decided to replace the old 0.0.1 version of Balbes by its more recent 1.0.0 version. We followed the steps described in README for Installing BALBES under Your CCP4 Package but this is not sufficient. Here is the error message we get: A package withe the name BALBES already exists Proceed Couldn't make version comparision Dismiss Installation of BALBES was not completed what else do we need to know to access Balbes from ccp4i (we are using ccp4 6.1.3, ccp4interface 2.0.6) thanks for your help, Magali Mathieu Service de Biologie Structurale Sanofi Aventis tel: (33)1 58 93 39 90 fax: (33)1 58 93 80 63
