[ccp4bb] Postdoctoral position in Xing Lab at UW-Madison

[Yongna Xing]

Postdoctoral Fellow
Laboratory of Dr. Yongna Xing

McArdle Laboratory of Cancer Research

Wisconsin Institutes for Medical Research (WIMR) II 6451
University of Wisconsin-Madison

 Highland Ave
Madison, WI 53705

Dear all,


A postdoctoral position on structural biology is available to investigate the 
mechanisms and functions of phosphatase signaling complexes and their disease 
mutations in cancer and intellectual disability. We combine cryo-EM, x-ray 
crystallography, cell biology, system biology, biochemistry, computational 
biology, and bioinformatics to gain critical knowledge on complex phosphatase 
signaling network dictated by both allosteric structured cores and versatile 
signaling motifs. The research is performed in a highly multidisciplinary 
setting with basic scientists with expertise on Cryo-EM, biochemistry, cell 
biology, bioinformatics and chemical biology. We are well equipped for 
multidisciplinary research, such as powerful GPU computer, liquid handling 
crystallization robot, and live cell imaging system. In addition, our lab is 
conveniently located near multiple shared facilities. Our research is built on 
collaborations with more than 10 groups from US and Europe as well as dynamic 
collaborations on campus in both basic and clinical research. UW-Madison has 
highly collaborative research environment that easily establish novel 
collaborations.

We are seeking productive, and motivated individuals with excellent 
organizational, interpersonal, and communication skills. We expect our 
candidates have strong expertise in either cryo-EM or x-ray crystallography, 
and protein biochemistry. We also expect our candidates feel comfortable to 
apply system biology and in-house bioinformatic tools and work both 
independently and by collaboration toward personalized medicine for phosphatase 
diseases.



The starting salary for promising candidate will be $48,000 or above.



Review of applications will begin immediately and continue until the position 
is filled. To apply: Please send a cover letter, CV and the names and contact 
information for three references to Dr. Yongna Xing via email: 
x...@oncology.wisc.edu.



Under-represented minorities are encouraged to apply.





Warm regards,


Yongna



Yongna Xing, PhD

Associate professor of oncology

McArdle Laboratory for Cancer Research

WIMR II 6451

School of Medicine and Public Health

 Highland Avenue

University of Wisconsin-Madison

Madison, WI 53705


Tel: 608-262-8376

Email: x...@oncology.wisc.edu


https://mcardle.wisc.edu/who-we-are/mcardle-faculty/yongna-xing-phd

https://mcardle.oncology.wisc.edu/xing/



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[ccp4bb] Two tenure-track faculty openings at Univ. of Missouri Biochemistry

[Tanner, John J.]

Dear Colleagues,

My department has two tenure-track faculty openings.

Review of applications will begin on November 15, 2019.

Click the link below for more information.

https://biochem.missouri.edu/open-positions/

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A




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[ccp4bb] PhD position in the structural mechanisms of ubiquitin signalling

[Sonja Lorenz]

The ubiquitin signalling research group headed by Sonja Lorenz at Rudolf 
Virchow Center for Experimental Biomedicine, Würzburg, Germany

is recruiting a PhD student

 
The Lorenz lab explores fundamental mechanisms of how posttranslational 
modifications encode specificity in cellular signaling with a particular focus 
on the ubiquitin system. Our lab combines cryo-EM and X-ray crystallography 
with biophysical, biochemical, and cell biological analyses.

We are supported by the EMBO Young Investigator Program, the Emmy Noether 
Program of the German Research Foundation, the Mildred Scheel Cancer Center, 
research unit FOR2314 (“Therapeutic windows”), and the graduate training group 
GRK2243 (“Understanding ubiquitylation”). The successful candidate will have 
the opportunity to be affiliated with GRK2243 and investigate the structural 
mechanisms of an exciting class of enzymes essential for infectious disease.

The Rudolf Virchow Center is a highly competitive international research 
institute with an outstanding infrastructure. The Lorenz lab has in-house 
access to state-of-the-art instrumentation in cryo-EM (Titan Krios), X-ray 
crystallography, and an extensive range of modern biophysical and cell 
biological equipment. We are integrated into a stimulating environment that 
includes the Helmholtz Institute for RNA-based Infection Research, the Max 
Planck Research Group in Systems Immunology, the Biocenter, the Institute for 
Molecular Infection Biology, and the University Hospital in Würzburg.

Würzburg is located in the beautiful, wine-growing area of Franconia, in 
proximity of Frankfurt (1 hour by train) and Munich (2 hours).

Applicants should have an MSc or equivalent degree in the life sciences or a 
related discipline and a passion for structural biology and protein 
biochemistry. Preliminary experience with cryo-EM or X-ray crystallography 
would be great, but is not strictly required. Good English language skills are 
necessary; knowledge of German is not necessary.

The position can begin immediately or upon mutual agreement. Salary will be 
according to the German TVL scale. In case of equivalent qualifications, 
disabled applicants will be preferentially considered.

Applications and inquiries should be sent to Sonja Lorenz by email and include 
a letter of motivation stating research interests and expertise, a CV, and the 
contact information of at least two references. 
Application deadline: 1 November 2019. Review of applications will begin 
immediately until the position is filled.

http://virchow-zentrum.uni-wuerzburg.de/lab_pages/slorenz/ 

twitter @ SLorenzLab

 
Sonja Lorenz, PhD
Rudolf Virchow Center for Experimental Biomedicine
University of Würzburg, 97080 Würzburg, Germany
E-mail: sonja.lor...@virchow.uni-wuerzburg.de 





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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Image Processing Workshop - Nov. 18-20, 2019

[Dunn, Lisa B.]

S2C2 Workshop - Image Processing, November 18-20, 2019
Stanford-SLAC Cryo-EM Center (S2C2) will offer a training workshop held at SLAC 
National Accelerator Laboratory between November 18 and 20, 2019. This workshop 
will include all steps of image reconstruction and the practical use of 
software for single particle image reconstruction available under Scipion. This 
workshop will consist of three days of lectures and hands-on training sessions 
led by Profs. David DeRosier, Jose Maria Carazo, Georgios Skiniotis and 
colleagues. The practical sessions will be conducted via cloud computing 
accounts and is only available on-site to a limited number of participants. 
Zoom teleconferencing will be available for the lectures and demonstration of 
the practical material  but will not have a practical participation option. If 
you are interested, you may apply before October 31, 2019.

There is no fee for this workshop.  If you are interested, please apply by 
October 31, 2019.   https://cryoem.slac.stanford.edu/s2c2/training/workshops


The Organizers (Wah Chiu, Georgios Skiniotis, Britt Hedman, Michael Schmid)



The S2C2  https://cryoem.slac.stanford.edu/s2c2/ is supported by the National 
Institutes of Health Common Fund Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] Cryo-EM Junior Group Leader Position in Berlin

[Oliver Daumke]

Dear PostDocs working in the field of cryo-EM,

Please find below a job advertisement for a cryo-EM junior group leader 
position in Berlin at the MDC.


Much looking forward to your applications !

All the best,

Oliver


The Max Delbrueck Center for Molecular Medicine (MDC) in Berlin, a 
leading biomedical research institute and a member of the Helmholtz 
Association of German Research Centers, invites applications for an
Independent Group Leader Position in Cryo-Electron Microscopy. We are 
seeking for outstanding postdoctoral researchers with a background in 
cryo-electron microscopy to develop their own research program and 
contribute to the establishment of cutting edge cryo-EM applications in 
Berlin. Integrative structural biology approaches with a focus on 
cryo-electron tomography are particularly welcome.


In close collaboration with the Charité Universitätsmedizin Berlin and 
its new cryo-EM core facility on our campus in Berlin-Buch, we provide 
access to state-of-the-art infrastructure for cryo-electron tomography, 
including a Titan Krios with a Gatan K3 Direct Electron Detector, an 
Aquilos Focused Ion Beam Scanning Electron Microscope and a Cryo 
Correlative Light Electron Microscope. The successful applicant will 
benefit from a highly collaborative and vibrant scientific environment 
within the MDC and its partner institutions in the Berlin region. He or 
she has also access to our platforms for X-ray crystallography, advanced 
light microscopy, drug screening and proteomics, amongst others. NMR 
expertise is available at the neighbouring Leibniz-Institute for 
Molecular Pharmacology. The offered independent group leader position 
(principal investigator position) includes generous funding for 5 years 
with an option for extension or tenure upon evaluation.


For information about the MDC, please visit our web site 
(www.mdc-berlin.de). For enquiries about the position, please contact 
Cornelia Maurer (mau...@mdc-berlin.de). For scientific questions, please 
contact Oliver Daumke (oliver.dau...@mdc-berlin.de).


The MDC is committed to diversity and actively supports equal 
opportunities for all employees regardless of their origin, religion, 
ideology, disability, age or sexual identity. We look forward to 
applications from people who are open-minded and enjoy working in joint 
teams. The MDC is certified by the “work and family” audit and provides 
an inclusive and family friendly environment. Applications from women 
are explicitly encouraged. Applications should be submitted to the 
web-based application portal (https://application.mdc-berlin.de) by 
November 25, 2019 indicating the registration number 11157/2019 and 
include a curriculum vitae, list of publications, and an outline of 
present and future research plans (not longer than 5 pages in total). 
Please submit your application in a single file, pdf format, maximum 
size 8 MB.



--
Prof. Dr. Oliver Daumke
Max-Delbrück-Centrum for Molecular Medicine
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Tel.: 0049-30-94063425
Fax.: 0049-30-94062548



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[ccp4bb] advert for PostDoc position @Singapore

[SR Bharath]

Dear Colleagues,



We are seeking an enthusiastic and self-motivated postdoctoral research
fellow to study proteins involved in maintaining genome stability and the
Hippo signaling pathway. We take a combinatorial approach of molecular
biology, biochemical and biophysical methods, and structural biology
(macromolecular crystallography and electron cryomicroscopy). ­Significant
aspects of our projects have translational potential. The candidate is
expected to be involved in the development of small molecules/peptides for
cancer therapeutics.



Singapore is an excellent environment to do research with many research
groups close by in Biopolis [https://www.a-star.edu.sg/imcb]. A*STAR offers
highly competitive salaries with benefits including housing allowance and
1-3 months performance bonus.



Requirements:

·   PhD in biochemistry, biophysics, molecular & cell biology or
in  medicinal
chemistry

·   Practical experiences in structural biology (Electron
Cryomicroscopy and/or X-ray crystallography) or in medicinal chemistry

·   Good publication record

·   Competent in scientific writing



Interested applicants should send a CV and three confidential letters of
reference to: Prof. Haiwei Song (Email: *hai...@imcb.a-star.edu.sg
*),
Institute of Molecular and Cell Biology, A*STAR, Singapore.


Cheers,

Bharath



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Re: [ccp4bb] *** WARNING SUSPECTED VIRUS, SPAM or SCAM *C* [ccp4bb] how to define connectivity, bond types... in PDB files

[Paul Emsley]

Hi Fred,

On 14/10/2019 08:46, Fred Vellieux wrote:


I am working on "non-standard" small molecules (docking to protein structures). To generate pdb files I use 
molview.org (for drawing and then generating .mol files, see the attached picture file molecule.jpg)


You can draw and edit mol files in Coot. If I am allowed to bang on my own drum, I'd say that the 2D 
representations are rather high quality.


 then 
babel to convert to the pdb format

Convert your mol files to 3D PDB files (or mmCIF) using Acederg, Pyrogen, or 
Grade.

Pressing "Accept" should run one of those programs - depending on your binary 
distribution.



Even though the geometry is correctly defined at the stage of molview.org, the "definitions" (of 
connectivities, bond types etc) are all lost during the conversion.


The pdb files give the type of pictures enclosed in coot or pymol (attachments) that aren't suitable for 
publication purposes. 


 - the bond lengths are 1.0 I suppose. Coot uses a default bond length of 1.5 so if you look at the 
2D mol file directly it will appear moderately sane.


Paul.



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[ccp4bb] summary: how to define connectivity, bond types... in PDB files

[Fred Vellieux]

Dear all,

These are the replies received so far:

Daniel Rigden (U. of Liverpool) suggested to do the conversion using 
https://www.webqc.org/molecularformatsconverter.php . It didn't work for 
me, the small molecule may be too complex (error message when reading 
the .mol file);


Petr Kolenko (Czech Technical University in Prague) suggested to use the 
smiles small molecule definition format. molview.org provides a smiles 
string in the place where the URL appears when drawing the molecule and 
then converting it from 2D to 3D.


I located an online smiles translator 
(https://cactus.nci.nih.gov/translate/ ) and used it to generate a pdb 
file that appears to satisfy Pymol (see enclosed screen capture). I 
don't yet know if Pymol will still be happy after docking;


Stephane Rely (ENS Lyon) suggested the use of the prodrg server, and 
drawing the molecule with JME. I haven't tried this approach yet;


Finally, Massimo Degano (San Raffaele Scientific Institute in Milano) 
suggested to read in the pdb in Avogadro and writing it out, with CONECT 
cards written automatically. This didn't work on my system (Avogadro 
doesn't install due to Qt not being in found at the cmake stage, 
although it is present on my system)


Thank you for the prompt responses.

Fred.




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[ccp4bb] Cryo-EM beamline scientist position at CBI / IGBMC, Strasbourg

[Bruno KLAHOLZ]

Dear all,

here is an announcement for a cryo-EM beamline scientist position at the Centre 
for Integrative Biology, Strasbourg, France.

With best regards,

Bruno Klaholz



Cryo-EM beamline scientist position:
The IGBMC/CBI is seeking a experienced scientist to participate in running the 
cutting-edge EM facilities at the Centre for Integrative Biology (CBI) at 
IGBMC, Illkirch/Strasbourg, France, while also participating in the on-site 
scientific projects.


The CBI provides a leading-edge scientific and technological environment in 
integrated structural biology to address the structure and function of 
biological systems, notably on gene expression, from the atomic, molecular to 
the tissue scales. The CBI http://www.igbmc.fr/grandesstructures/cbi/, hosts 
the French and European Infrastructures for Integrated Structural Biology, 
FRISBI http://frisbi.eu/  and Instruct https://www.structuralbiology.eu/  which 
comprises advanced electron microscopy facilities equipped with cutting-edge 
instrumentation such as Titan Krios and Polara cryo electron microscopes, cryo 
Focused Ion Beam Scanning Electron Microscope (FIB/SEM) and super-resolution 
fluorescence microscopy 
http://frisbi.eu/centers/instruct-center-france-1-igbmc/cryo-electron-microscopy/.
 The Titan Krios microscope is equipped with Cs corrector, Falcon 3 camera, GIF 
energy filter, K3 camera and phase plate. In addition, the EM facility has a 
suite of associated equipments for sample preparation and dedicated computing 
resources for image processing and 3D reconstruction by single particle cryo-EM 
and cryo electron tomography (cryo-ET). For projects and publications of the 
associated teams see http://igbmc.fr/research/department/3/

Applications should be sent via the CNRS portal 
https://emploi.cnrs.fr/Offres/CDD/UMR7104-GUEBUR-004/Default.aspx
including CV, list of publications, names of 3 referees and motivation letter. 
Please contact me at klah...@igbmc.fr if you have 
questions.


###
Bruno P. Klaholz
Centre for Integrative Biology
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 1258
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.369.48.52.78
Tel. inside France: 03.69.48.52.78
websites:
http://igbmc.fr/Klaholz
http://www.igbmc.fr/grandesstructures/cbi
http://frisbi.eu
http://instruct-eric.eu




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[ccp4bb] Postdoctoral position for XFEL crystallography/spectroscopy at Berkeley Lab

[Jan Kern]

We are looking for a postdoctoral fellow to study metalloenzymes using
X-ray crystallography and spectroscopy at X-ray free electron lasers. The
fellow will work in the Kern/Yachandra/Yano group (
http://www2.lbl.gov/vkyachan/ and
http://biosciences.lbl.gov/profiles/jan-florian-kern/) at Berkeley Lab’s
Molecular Biophysics & Integrated Bioimaging Division. We have been
conducting a number of XFEL experiments on several different systems and
recent publications include:

Chatterjee et al J Synchr Rad 2019
https://onlinelibrary.wiley.com/doi/abs/10.1107/S1600577519007550
Kern et al, Nature 2018 https://www.nature.com/articles/s41586-018-0681-2
Fuller et al, Nature Methods 2017
http://www.nature.com/nmeth/journal/v14/n4/abs/nmeth.4195.html
Kubin et al Structural Dynamics 2017
https://aca.scitation.org/doi/10.1063/1.4986627
Young et al Nature 2016
https://www.nature.com/nature/journal/v540/n7633/full/nature20161.html

Ideally the candidate should have a good background in one or more of the
following fields:
- Macromolecular crystallography
- X-ray spectroscopy of dilute transition metal systems/biological systems.
- Designing of experimental setups for use at synchrotron/X-ray free laser
facilities.

Details of the position and instructions how to apply can be found here:
https://lbl.referrals.selectminds.com/jobs/xfel-postdoc-for-crystallography-spectroscopy-2214

For informal inquiries please feel free to contact me: jfk...@lbl.gov

Thanks,

Jan Kern


Jan Kern
Research Scientist
Molecular Biophysics and Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
One Cyclotron Road, MS 66-327
Berkeley, CA 94720
USA
phone: 510-486-4330 / -7437
e-mail: jfk...@lbl.gov



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