[ccp4bb] 8th workshop on Neutron Scattering Applications in Structural Biology

[Meilleur, Flora]

First announcement

8th Workshop on Neutron Scattering Applications in Structural Biology
Oak Ridge, TN. June 5 - June 9, 2017

Detailed information can be found on the workshop web page: 
https://conference.sns.gov/event/66/
Application deadline: April 22, 2017

The workshop on Neutron Scattering Applications in Structural Biology aims at 
enabling structural biologists to fully exploit the latest instrumentation and 
software development at the SNS and HFIR facilities at Oak Ridge National 
Laboratory. Attendees will participate in lectures and tutorials focusing 
exclusively on neutron techniques applied in structural biology. The workshop 
is designed for graduate students, post-doctoral fellows and faculty new to or 
with limited experience of neutron scattering.

Travel and accommodation expenses are supported for selected participants from 
the United States. International applications are welcome - however the course 
organization is not able to support travel or accommodation.

The number of participants will be limited to 15. There is no registration fee 
for all selected participants.

The application package consisting of 1) Information form, 2) CV, 3) Applicant 
motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support 
(for graduate students only; 1/2 to 1 page), should be sent electronically to 
meille...@ornl.gov before April 22, 2017.

Flora Meilleur, Ph. D
Associate Professor, Molecular and Structural Biochemistry
North Carolina State University
Neutron Sciences Directorate
Oak Ridge National Laboratory
Phone: 865-242-5747

[ccp4bb] postdoctoral position at Centre for Integrative Biology, IGBMC, Strasbourg

[Bruno KLAHOLZ]

Dear all,



we are seeking an enthusiastic post-doctoral researcher to join the Klaholz 
group at the Centre for Integrative Biology, IGBMC, Illkirch, France 
http://igbmc.fr/Klaholz



We are studying the structure and function of protein complexes through 
integrated structural biology and notably by high resolution cryo-EM. We are 
looking for a highly enthusiastic and motivated scientist with relevant 
experience in structural biology of DNA/RNA-protein complexes, ideally with 
good experience in cryo electron microscopy. For further details please see 
below.



With best regards,



Bruno Klaholz









Some recent publications:

-  I. Orlov, A. G. Myasnikov, L. Andronov, S. K. Natchiar, H. Khatter, B. 
Beinsteiner, J-F. Ménétret, I. Hazemann, K. Mohideen, K. Tazibt, R. Tabaroni, 
H. Kratzat, N. Djabeur, T. Bruxelles, F. Raivoniaina, L. di Pompeo, M. Torchy, 
I. Billas, A. Urzhumtsev & B. P. Klaholz. The integrative role of cryo electron 
microscopy in molecular and cellular structural biology. Biol Cell., 2016, Oct 
12. doi: 10./boc.201600042.

-  A. G. Myasnikov, S. K. Natchiar, M. Nebout, I. Hazemann, V. Imbert, H. 
Khatter, J.-F. Peyron & B. P. Klaholz. Structure-function insights reveal the 
human ribosome as a cancer target for antibiotics. Nat Commun., 2016, 7, 12856. 
doi: 10.1038/ncomms12856.

-  A. Simonetti, J.-F. Ménétret, F. Martin, A. G. Myasnikov, Q. Vicens, L. 
Prongidi-Fix, S. K. Natchiar, B. P. Klaholz & G. Eriani. Ribosomal 18S rRNA 
base pairs with mRNA during eukaryotic translation initiation. Nat Commun., 
2016, 7, 12622. doi: 10.1038/ncomms12622.

-  L. Andronov, I. Orlov, Y. Lutz, J-L. Vonesch & B. P. Klaholz. ClusterViSu, a 
method for clustering of protein complexes by Voronoi tessellation in 
super-resolution microscopy. Sci. Rep. 2016, 6, 24084. doi: 10.1038/srep24084.

-  L. Andronov, Y. Lutz, J-L. Vonesch & B. P. Klaholz. SharpViSu: integrated 
analysis and segmentation of super-resolution microscopy data. Bioinformatics, 
2016, 32, 2239-2241. doi: 10.1093/bioinformatics/btw123.

-  B. P. Klaholz. Structure sorting of multiple macromolecular states in 
heterogeneous cryo-EM samples by 3D multivariate statistical analysis. Open 
Journal of Statistics, Special Issue on Multivariate Statistical Analysis, 
2015, 5, 820-836. http://dx.doi.org/10.4236/ojs.2015.57081.

-  B. Beinsteiner, J. Michalon & B. P. Klaholz. IBiSS, a versatile and 
interactive tool for integrated sequence and 3D structure analysis of large 
macromolecular complexes. Bioinformatics, 2015, 31, 3339-3344. doi: 
10.1093/bioinformatics/btv347.

-  H. Khatter, A. G. Myasnikov, K. Natchiar & B. P. Klaholz. Structure of the 
human 80S ribosome. Nature, 2015, 520, 640-5. doi: 10.1038/nature14427. Epub 
2015 Apr 22.

-  Z. A. Afonina, A. G. Myasnikov, V. A. Shirokov, B. P. Klaholz, A. S. Spirin. 
Conformation transitions of eukaryotic polyribosomes during multi-round 
translation. Nucleic Acids Res. 2015, 43, 618-28. doi: 10.1093/nar/gku1270.

-  A. G. Myasnikov, Z. A. Afonina, J-F. Ménétret, V. A. Shirokov, A. S. Spirin 
& B. P. Klaholz. The molecular structure of the left-handed supra-molecular 
helix of eukaryotic polyribosomes. Nat Commun., 2014, 5, 5294. doi: 
10.1038/ncomms6294.

-  M. Maletta, I. Orlov, P. Roblin, Y. Beck, D. Moras, I. M. L. Billas & B. P. 
Klaholz. The palindromic DNA-bound USP/EcR nuclear receptor adopts an 
asymmetric organization with allosteric domain positioning. Nat Commun., 2014, 
5, 4139. doi: 10.1038/ncomms5139.



For ongoing projects and full publication list of the team see 
http://igbmc.fr/Klaholz



Our group is located at the Centre for Integrative Biology (CBI) at IGBMC, 
Illkirch/Strasbourg, France, which comprises cutting-edge cryo-EM facilities:

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 (cryo-FIB/SEM) and 
super-resolution fluorescence microscopy. The Titan Krios microscope is 
equipped with Cs corrector, Falcon 2 camera, GIF energy filter, K2 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).



Applications should be sent via email to 
klah...@igbmc.fr including CV, list of publications, 
names of 3 referees and 

Re: [ccp4bb] To delete main chain or not

[Debanu]

Hi Veronica,

Yes, it is okay to exclude few residues or even short stretches of 
loops/helices/strands if there is no reliable/convincing electron density for 
them even at low map contours because if there is no convincing density you 
cannot reliably model the local structure. 

However, if you refine with tight NCS, which you probably should do at this 
resolution unless there are significant differences in the 4 molecules, you can 
also choose to keep residues for which there is no reliable density in one of 
the molecules, provided those residues are well resolved in the other molecules 
and refine well (density, B-factors). Also use TLS refinement. 

Irrespective of which of the 2 options you choose, make sure to add a remark in 
the PDB header about the option chosen, so that others know what was done and 
if you write it up in a manuscript, describe it there as well.

Best,
Debanu Das.

> On Jan 10, 2017, at 3:30 AM, V F  wrote:
> 
> Dear all,
> I have a model with 4 molecules in asu. One of the domains is poorly
> ordered, weak density. Please see the screenshot with 2 panel (2
> chains side-by-side). My question: In the right panel:
> 1. Should I delete residues 653- 655?
> 2. Should the helix 689-702 be deleted? can I keep a few residues -
> orphaned? Is there a specific rule for these types of data.
> 
> The map was generated with Phenix/FEM contoured at 1.5 sigma. Data set
> at 2.8A. Many thanks for your advise.
> 
> I looked at many PDB models + density from EDS there are poorly
> defined regions. My chemistry based group has no experience on
> bio-structures.
> Veronica
> 

[ccp4bb] CCP4 Study Weekend Link for CCP4 Stream

[Charles Ballard]

Dear All

Here is the link for CCP4 Study Weekend


https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:4#


Charles

[ccp4bb] Post-doctoral position in cryo-EM/structural biology of multiprotein kinase signalling complexes

[Stefan Arold]

Dear All,

For those among you who don't like rain, please see the below posting for a
post-doctoral position in my group at KAUST.

With my best wishes for a happy and successful 2017!
Stefan

PS: I am at the CCP4 study weekend, with 'lunch byte' presentation on
Tuesday - in case potential candidates wish to catch me there.

Post-doctoral position in cryo-EM/structural biology of multiprotein kinase
signalling complexes

*Project:* Structural and functional analysis of a multiprotein kinase
signalling complex involved in mediating immune responses in eukaryotes.

*Methods:* Hybrid approaches in structural biology: cryo-EM, X-ray
crystallography, SAXS, NMR, computational methods, bioinformatics,
biophysics and biochemistry. Functional characterization on a cellular and
organismal level is carried out in close collaboration with the group of
Dr. Heribert Hirt (KAUST).

*Required skills*: Experience in protein expression, purification and
characterization; Expertise in structural methods, in particular cryo-EM
and X-ray crystallography. A high level of motivation and the ability to
work as part of a team are essential.

*Location:* Group of Stefan Arold at the King Abdullah University of
Science and Technology (KAUST). KAUST, founded in 2009, is located at the
shores of the Red Sea in Saudi Arabia. KAUST currently ranks nr. 1
worldwide in citations per faculty (QS World University Rankings 2015/2016)
and provides outstanding research facilities (incl. a Titan KRIOS with
direct detector, NMR spectrometers up to 950 MHz & in-house X-ray source).
KAUST has a community with more than 100 nationalities, pristine coral
reefs and about two hours of rain per year.

*Remuneration:* highly competitive salary, commensurate with experience,
and various benefits.

*Starting Date:* available from April 2017, but later starting dates can be
accomodated

*Contact: *Please send a CV, a statement of research experience and contact
information for at least two referees to stefan.ar...@kaust.edu.sa.


---

Stefan T. Arold, PhD

Division of Biological and Environmental Sciences and Engineering

Computational Bioscience Research Center (CBRC)

King Abdullah University of Science and Technology (KAUST)

Thuwal 23955-6900

Bldg 2, Level 4, Room 4275

Kingdom of Saudi Arabia

Em: stefan.ar...@kaust.edu.sa

https://strube.cbrc.kaust.edu.sa/