[ccp4bb] Postdoctoral Position at UC-Davis to study structures of tubulin biogenesis and polymerization regulators

[Jawdat Al-Bassam]

Dear Colleagues, 

An opportunity is available for a postdoctoral fellow to work with Jawdat 
Al-Bassam (http://microtubule.mcb.ucdavis.edu 
) at the Molecular Cellular Biology 
Department at the University of California at Davis. The Al-Bassam laboratory 
is focused on structural studies of assemblies regulating the biogenesis and 
polymerization of tubulin dimers and their impact on the polymerization of 
microtubules.  The projects aim to characterize tubulin regulation by 
multi-subunit complexes using biochemical reconstitution,  cryo-electron 
microscopy (cryo-EM) and x-ray crystallography.  We have a particular interest 
in determining structures of multi-subunit complexes using well-developed tools 
in the laboratory, and then we aim to test functional mechanisms using in vitro 
reconstitution with dynamic microtubules.  We are looking for an enthusiastic 
individual who thrives in a collaborative and supportive atmosphere. You should 
have a PhD in chemistry, biochemistry or biophysics and a desire to understand 
structures of multi-subunit macromolecular assemblies in relation to their 
functional mechanisms.  Expertise required include molecular cloning, 
recombinant protein production  using bacteria, insect and mammalian cells.  
The position would suit someone with a strong background  in X-ray 
crystallography who also wants to learn cryo-EM, or someone who already has 
experience in cryo-EM and single particle image analysis.  Please see our 
recent papers: https://elifesciences.org/articles/38922# 
, 
https://elifesciences.org/articles/08811 
. 

The Al-Bassam laboratory has extensive tools and setups for protein production, 
biochemical characterization, x-ray crystallography in addition to 
computational resources. The laboratory has full access to a well-supported 
UC-Davis BIOEM facility, which includes cryo-EM sample preparation, a 
semi-automated side-entry JEOL 2100F microscope, and a new 200 KV Glacios 
microscope equipped with an autoloader and a K3 detector.  UC-Davis is a member 
of the Bay Area Cryo-EM consortium with monthly access to Titan Krios 
microscopes for high resolution data collection. 

Please send any informal inquiries to jaw...@ucdavis.edu 
. Please include a cover letter, CV, statement of 
research accomplishments, and two to three reference letters.  

To apply and access full details of the position please visit: 
http://microtubule.mcb.ucdavis.edu  or 
https://recruit.ucdavis.edu/JPF02735 

sincerely   

Jawdat M Al-Bassam Ph.D.
Molecular Cellular Biology
University of California Davis


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Re: [ccp4bb] help with TNCS + MR

[Eleanor Dodson]

Sorry to plug MOLREP to a Phaser Q, but it does have some simple tNCS
functions which work well for
straightforward cases.

Something to consider:
tNCS can make spacegroup determination based on axial reflection absences
tricky so set a flag to test all SGS in the pointgroup.
For example: (A translation vector of (x,y,1/4) will mean that only
reflections (0,0,l) will be strong for l having a factor of 4 , ie
4,8,12,16,..)

And R factors are typivally higher for crystals with tNCS -- extensive
classes of reflections are weak..

Eleanor



On Thu, 14 Mar 2019 at 13:48, Randy Read  wrote:

> Dear Almu,
>
> We have a discussion on the Phaser Wiki about some of the possibilities
> for tNCS, what you should look for, and what Phaser can handle:
> http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry.
> As it explains, if you have one major peak in the native Patterson then
> everything will be pretty automatic, and it can even be straightforward if
> you have several peaks corresponding to multiples of the same underlying
> translation.  If you have some specific questions about your problem after
> you’ve read that and run Phaser on your problem, then let us know!
>
> Best wishes,
>
> Randy
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 14 Mar 2019, at 05:07, Almudena Ponce Salvatierra <
> maps.fa...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I have a dataset with strong TNCS and I would like to know if there are
> a "series of steps" that I could follow in order to find out whether I can
> solve my structure or not.
> >
> > I see on the Phaser wiki that structure determination in the presence of
> TNCS is not fully automated. which steps are those in which my intervention
> should be needed and what do I look for?
> >
> > It is the first time that I deal with this problem and I'd be immensely
> thankful if I could get some hints from those of you who have encountered
> it in the past or understand where in particular I should keep and eye on :)
> >
> > All the best,
> >
> > cheers,
> >
> > Almu
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
>
> 
>
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>



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[ccp4bb] HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop - HANDS 2019

[Meilleur, Flora]

2nd announcement

HANDS 2019
HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop
Oak Ridge, TN. June 9 - June 14, 2019

Oak Ridge National Laboratory, in conjunction with North Carolina State 
University, and support from the National Science Foundation and the Shull 
Wollan Center - a Joint Institute for Neutron Scattering, celebrates a decade 
of neutron scattering education in structural biology at ORNL with the HFIR/SNS 
Advanced Neutron Diffraction and Scattering workshop (HANDS 2019).

Detailed information can be found on the workshop web page: 
https://conference.sns.gov/hands2019/
Application deadline: April 29, 2019
Fellowships to support travel and accommodation are available. No registration 
fee.

The workshop 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. Participants of HANDS 2019 will become familiar with 
neutron techniques with hands-on experiments in sample preparation, 
crystallography, small angle scattering, reflectometry and neutron spin echo. 
The workshop is designed for graduate students, post-doctoral fellows and 
faculty with limited to no experience with neutron sciences.

Flora Meilleur, Ph. D
Neutron Scattering Scientist, Neutron Scattering Division
Oak Ridge National Laboratory
Associate Professor, Molecular and Structural Biochemistry
North Carolina State University




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Re: [ccp4bb] help with TNCS + MR

[Randy Read]

Dear Almu,

We have a discussion on the Phaser Wiki about some of the possibilities for 
tNCS, what you should look for, and what Phaser can handle: 
http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry.
  As it explains, if you have one major peak in the native Patterson then 
everything will be pretty automatic, and it can even be straightforward if you 
have several peaks corresponding to multiples of the same underlying 
translation.  If you have some specific questions about your problem after 
you’ve read that and run Phaser on your problem, then let us know!

Best wishes,

Randy

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 14 Mar 2019, at 05:07, Almudena Ponce Salvatierra  
> wrote:
> 
> Dear all, 
> 
> I have a dataset with strong TNCS and I would like to know if there are a 
> "series of steps" that I could follow in order to find out whether I can 
> solve my structure or not. 
> 
> I see on the Phaser wiki that structure determination in the presence of TNCS 
> is not fully automated. which steps are those in which my intervention should 
> be needed and what do I look for?
> 
> It is the first time that I deal with this problem and I'd be immensely 
> thankful if I could get some hints from those of you who have encountered it 
> in the past or understand where in particular I should keep and eye on :)
> 
> All the best, 
> 
> cheers, 
> 
> Almu
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 



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[ccp4bb] help with TNCS + MR

[Almudena Ponce Salvatierra]

Dear all,

I have a dataset with strong TNCS and I would like to know if there are a
"series of steps" that I could follow in order to find out whether I can
solve my structure or not.

I see on the Phaser wiki that structure determination in the presence of
TNCS is not fully automated. which steps are those in which my intervention
should be needed and what do I look for?

It is the first time that I deal with this problem and I'd be immensely
thankful if I could get some hints from those of you who have encountered
it in the past or understand where in particular I should keep and eye on :)

All the best,

cheers,

Almu



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[ccp4bb] OPEN POSTDOC POSITION: PROTEIN STRUCTURAL BIOLOGIST

[Jitka Sedláčková]

We are seeking a highly motivated scientist for an EU-funded postdoctoral
position in protein structural biology for an experimental team at Loschmidt
Laboratories, Masaryk University, Brno, Czech Republic 
(https://loschmidt.chemi.muni.cz/peg/). We conduct basic research in enzymology 
and fight acute stroke, cancer and Alzheimer’s disease.

JOB DESCRIPTION:
Perform protein expression, purification and biophysical characterization. 
Design and perform protein crystallization experiments.
Collect X-ray diffraction data and determine protein-ligand complex structures.
Adapt emerging structural techniques: nanocrystallography and cryo-EM.
Work in a friendly, inspiring and highly collaborative environment.
Opportunities for further training, personal growth and benefits package.

CANDIDATE PROFILE:
PhD in structural biology, molecular biology, biochemistry or biophysics.
Experience with protein expression and purification.
Previous experience with protein structural techniques.
Experience with biophysical and biochemical protein characterization.
Willingness to learn new techniques: nanocrystallography and cryo-EM.
Ability to develop new concepts; goal-oriented and problem-solving skills.
Good proficiency in English.

APPLICATIONS:
Curriculum Vitae and motivation letter.
Two letters of recommendation.
Send your application to Jitka Sedlackova at jitkasedlack...@mail.muni.cz

SELECTED PAPERS:
J. Am. Chem. Soc. 140: 17999, 2018 ACS Catalysis 8: 9420, 2018
J. Am. Chem. Soc. 137: 4988, 2015 ACS Catalysis 6: 7597, 2016
Chem. Rev. 113: 5871, 2013  Curr. Opin. Chem. Biol. 19: 8, 2014 
Angewandte Chemie 52: 1959, 2013Nature Chem. Biol. 10: 428, 2014

-
Jitka Sedláčková, PhD

Loschmidt Laboratories
RECETOX, Masaryk University
ICRC, St. Anne's University Hospital
Tel. +420 54949 3041



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[ccp4bb] Cryo-EM Facility Manager Position available at CUHK(SZ)

[Prof. Stjepanovic Goran (SSE)]

The Chinese University of Hong Kong, Shenzhen CUHK(SZ) seeks for a full-time 
Cryo-EM Facility Manager.

Dear all,

The Cryo-EM platform at The Chinese University of Hong Kong, Shenzhen and the 
Kobilka Institute of Innovative Drug Discovery (KIIDD) seeks a Ph.D.-level 
scientist to serve as Cryo-EM facility manager. The successful candidate will 
join an interdisciplinary, collaborative research community and will play a 
leading role in overseeing the day-to-day operation of Cryo-EM facility, serve 
on an advisory committee of faculty and be responsible for application and 
development of Cryo-EM technologies for high-resolution structural 
determination.

Responsibilities include, but are not limited to:


  *   General maintenance of microscopes, including the alignment
  *   Oversee and coordinate the instrument preventative maintenance
  *   Maintaining consumables and Cryo-EM sample preparation equipment
  *   Providing practical training and application service for Cryo-EM users
  *   Assisting users in EM sample preparation, data collection, and data 
processing
  *   Ensure the facility is in compliance with EH&S


The CUHK(SZ) Cryo-EM platform is housed at KIIDD, and includes two FEI Titan 
Krios G3i (with K3 and Falcon III direct detector; Volta Phase Plate; Gatan 
Energy Filter). The facility also houses FEI Talos (120 kV) TEM, and dedicated 
high performance computing resources for data processing and temporary storage.

Qualifications and Requirements:
Applicants should have a Ph.D. degree in biology, physics, material science or 
a related field, and extensive experience in Cryo-EM or EM.

How to Apply:
Candidates should e-mail the application and include a cover letter, curriculum 
vitae, and the names and contact information of three references to Dr. Goran 
Stjepanovic:goranstjepano...@cuhk.edu.cn

An internationally competitive salary, working environment and living 
conditions with fringe benefits are provided according to relevant regulations 
and policies for talent introduction by CUHK(SZ) and the prevailing labor laws 
applicable in the PRC. Review of applications will begin immediately and will 
continue until position is filled.




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[ccp4bb] Ultrafast X-ray Summer School (UXSS2019) in Hamburg: June 17-21

[Thomas White]

[second announcement - registration extended until 22 March 2019 -
next week!]

Dear  All,

The Ultrafast X-ray Summer School UXSS2019 will take place at the
Center for Free Electron Laser Science (CFEL) in Hamburg, Germany, June
17-21, 2019.

UXSS is an annual event jointly organized by the Center for
Free-Electron Laser Science (CFEL) in Hamburg and the Stanford PULSE
Institute. UXSS is intended to introduce students and postdocs to the
latest science that is enabled by novel X-ray Free Electron Lasers. The
program will be highly interdisciplinary, with topics ranging from
materials physics to structural biology. The list of confirmed speakers
can be found below.  There will also be a coursework exercise involving
a mock proposal for European XFEL, with the help of experienced mentors.

The UXSS2019 website is now online with more information:
https://conferences.cfel.de/uxss_2019

Registration is open: https://indico.desy.de/indico/event/22369.
Registration will continue until March 22, with rolling acceptance.
Financial support for UXSS2019 is very kindly provided by the Joachim
Herz Stiftung and the Hamburg Centre for Ultrafast Imaging (CUI),
meaning that participants will be asked to pay a registration fee of
only 100 EUR. Limited participation scholarships to cover travel and
lodging costs are available. You can specify on the registration
website why you need a scholarship to participate.

We hope to see you in Hamburg this summer!

Michael Sentef (CFEL) and Thomas Wolf (PULSE)
Co-chairs, UXSS2019

Lecturers:
Henry Chapman (Hamburg University/DESY)
Frank de Groot (Utrecht University)
Arianna Gleason (SLAC)
Giorgio Margaritondo (EPFL Lausanne)
Brian Moritz (SLAC)
Nina Rohringer (Hamburg University/DESY)
Simon Wall (ICFO Barcelona)
Oriol Vendrell (Heidelberg University)
Junko Yano (LBL Berkeley)



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[ccp4bb] Biochemistry Postdoctoral Position at Imperial College London - Speck Lab

[Speck, Christian]

dear all,



Application deadline Tuesday March 26th.


a postdoctoral position is available at Imperial College London.



The Speck Lab works on the mechanism of eukaryotic chromosome replication. We 
are looking for a passionate researcher interested in investigating molecular 
machines.
The ideal candidate will have  extensive expertise in Biochemistry and/or 
Structural Biology . The post holder will explore fundamental mechanism in DNA 
replication using biochemical approaches and work with another group member to 
determine the structure of replication complexes by cryo-EM.

Research framework and support structure:

1.)The group consists of >10 members, 8 postdocs, 2 students, lab manager 
and technician.

2.)The lab is fully equipped for biochemistry (2 AKTAs, multiple 
temperature controlled shakers), two freezer mills, Biacore T100 and generously 
supported by the Wellcome Trust and multiple BBSRC grants.

3.)Access to state-of-the-art facilities including Mass Spectrometry, 
Structural Biology and Bioinformatics.

4.)The candidate will receive direct mentoring by the group head on grant 
applications, writing of manuscripts and project design.

5.)We have direct access to a local cryo-EM facility with a 200KV FEG 
microscope and the LonCEM facility with a Krios (K3 & Falcon 3 detectors, phase 
plate, energy filter,..).

Interested individuals are welcome to contact me directly for more information.

Best,
Christian
chris.sp...@imperial.ac.uk

here are a few links:

The Wellcome Trust funded 2-year position:

https://www.nature.com/naturecareers/job?id=677203

The group:

http://www.specklab.com/

Closing date: 26 March 2019


Selected papers:

Noguchi Y*, Yuan Z*, Bai L*, Schneider S, Zhao G, Stillman B#, Speck C#, Li H# 
(2017) Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging 
strand DNA extrusion model PNAS, Nov 7;114(45):E9529-E953

Riera A, Barbon M, Noguchi Y, Reuter LM, Schneider S, Speck C (2017) From 
structure to mechanism - understanding initiation of DNA replication Genes & 
Development, Jun 1;31(11):1073-108

Yuan Z*, Riera A*, Bai L*, Sun J*, Nandi S, Spanos C, Chen ZA, Barbon M, 
Rappsilber J#, Stillman B#, Speck C# and Li H# (2017) Structural basis of 
MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1 Nature Structure & 
Molecular Biology, Mar;24(3):316-32

Chang F, Riera A, Evrin C, Sun J, Li H, Speck C*, Weinreich M* (2015) Cdc6 
ATPase activity disengages Cdc6 from the pre-replicative complex to promote DNA 
replication eLife, Aug 25;4

Samel AS, Fernández-Cid A, Sun J, Riera A, Tognetti S, Herrera MC, Li H, Speck 
C (2014) A unique DNA entry gate for regulated loading of the eukaryotic 
replicative helicase onto DNA Genes & Development, Aug 1;28(15):1653-6

Sun J*, Fernandez-Cid A*, Riera A*, Tognetti S, Yuan Z, Stillman B#, Speck C#, 
Li H# (2014) Structural and mechanistic insights into Mcm2-7 double-hexamer 
assembly and function Genes & Development, Oct 15;28(20):2291-30

Sun J*, Evrin C*, Samel S, Fernández-Cid A, Riera A, Kawakami H, Stillman B#, 
Speck C#, Li H# Cryo-EM structure of a helicase loading intermediate containing 
ORC-Cdc6-Cdt1-MCM2-7 bound to DNA (2013) Nature Structure & Molecular Biology, 
August 5, (20), 944-951

Fernández-Cid A, Riera A, Tognetti S, Herrera MC, Samel S , Evrin C, Winkler C, 
Gardenal E,   Uhle S, Speck C. (2013) An ORC/Cdc6/MCM2-7 complex is formed in a 
multistep reaction to serve as a platform for MCM2-7 double-hexamer formation  
Molecular Cell, Volume 50, Issue 4, 577-588, 18 April


__

Professor Christian Speck, PhD, FRSB
Chair in Genome Biochemistry & Molecular Biology
Wellcome Trust Investigator

Imperial College London
Faculty of Medicine
Institute of Clinical Sciences (CRB room 3006)
Hammersmith Hospital Campus
Du Cane Road
London W12 0NN

Tel: 0044 20 8383 3387
Mobile: 0044 796 181 5557
Skype ID: dna_rep

email: christian.sp...@imperial.ac.uk
website: www.specklab.com
Imperial College website: 
www.imperial.ac.uk/people/chris.speck

[http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtvm050463.jpg]
 [cid:image002.png@01D33B79.8BEFDA70]




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[ccp4bb] Reminder: 4. User Call for MAX IV BioMAX beamtime, period Sept. 2019- Feb. 2020, deadline March 19, 2019

[Uwe Müller]

Dear all,
MAX IV in Lund, Sweden has opened the 4. user call to receive proposals 
requesting beamtime at BioMAX for the period September 2019 - February 2020.

In order to submit a new proposal, please visit this page:

https://www.maxiv.lu.se/users/proposal-calls/

BioMAX is working in regular user operation and is providing 8-24h beamtime to 
individual users or BAG user groups. Within the next beam period we are aiming 
to initiate the remote beamline operation as an additional access scheme to the 
international user community. The beam line is under continuous commissioning 
and will offer the following features during the next user period:

• Variable beam focus down to 20x5 µm^2 at the sample position at full photon 
flux (can be further reduced by apertures down to 5x5 µm^2)
• 2 x 10^13 Phot/sec at 250 mA ring filling at sample position
• Standard exposure time 11 msec / frame, corresponding to 10-60% 
transmission
• Tuneable energy range 5-20 keV
• MAD capabilities
• Raster scan mode
• Helical scan mode
• Serial crystallography applications using high viscosity extrusion 
injector and fixed target scanner (MD3 based)
• Sample changer operation using Uni-pucks, < 25 sec sample exchange time
• Eiger 16M hybrid pixel detector 130 Hz frame rate for 16M mode
• MD3-micro diffractometer, 150 nm sphere-of-confusion for micro-crystal 
centring
• HC-lab crystal dehydration device with fast nozzle changer for crystal 
dehydration and room temperature data collections
• MXCuBE3 experiment control software & ISPyB database support
• Automatic data processing during data collection
• Standard crystallographic software installed
• >1000 core HPC environment available online and offline access
• Sample preparation laboratory for crystal handling
• S1 bio-safety level bio-laboratory in close vicinity

MAX IV is member of the EU access project iNEXT, which also supports travel and 
accommodation for international user groups (See also: 
http://www.inext-eu.org). On campus, we have a guesthouse available, which can 
be booked via MAX IV before the beamtime as well.
We are looking forward for your beamtime proposals and the collaboration during 
your stay at MAX IV.


Uwe & the MAX IV MX-team!


Uwe Mueller
Group manager Macromolecular Crystallography
BioMAX beam line manager

MAX IV Laboratory
Lund University
Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 224 84 Lund, Sweden
Mobile:  +46(0)730-655268
E-mail: uwe.mul...@maxiv.lu.se
Url: www.maxiv.se
VAT No.: SE 2021 0032 1101









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