[ccp4bb] I

[Steiner, Roberto]

>From my iPhone

[ccp4bb] Postbac position in membrane protein structure and function at the NIH

[Anirban Banerjee]

Dear all,

I am looking for a postbac for a membrane protein structure-function project
in my lab at the NIH starting sometime this summer. The NIH Postbac IRTA
program provides recent college graduates who are planning to apply to
graduate or professional (medical/dental/pharmacy) school an opportunity to
spend one or two years performing full-time research at the NIH.

For this position I am looking for someone who has experience with protein
purification, has good organizational skills and work ethics, and the right
mindset to pay attention to nitty-gritty details that
are essential for working with membrane proteins. The candidate should apply
to the NIH Postbac Program (https://www.training.nih
.gov/programs/postbac_irta)  and get in touch with me as well. Postbac
candidates
have to be US citizens or permanent residents.

Thanks very much.

Anirban

[ccp4bb] Job Posting request for Johnson & Johnson

[Meghan jobtarget]

Janssen Research and Development, L.L.C., a member of Johnson and Johnson's
Family of Companies, is recruiting for a Post-Doctoral Scientist, Biologics
Research in Spring House, PA. This Post-Doctoral position will be a two
year assignment.



At the Janssen Pharmaceutical Companies of Johnson & Johnson, what matters
most is helping people live full and healthy lives. We focus on treating,
curing and preventing some of the most devastating and complex diseases of
our time. And we pursue the most promising science, wherever it might be
found.


Janssen Research & Development, LLC discovers and develops innovative
medical solutions to address important unmet medical needs in oncology,
immunology, neuroscience, infectious diseases and vaccines, and
cardiovascular and metabolic diseases. Please visit
http://www.JanssenRnD.com  for more
information.



We are Janssen. Our mission drives us. Our patients inspire us. We
collaborate with the world for the health of everyone in it.



Janssen R&D, LLC is looking for a self-motivated post-doctoral scientist to
study mechanisms of action for biologic therapeutics and their targets.
The successful candidate will apply structural biology approaches to
biologics and biologic/target complexes.  This position will give the
candidate exposure to many aspects of biologic discovery and development.
The candidate is expected to publish the results of his/her project(s).

 Job Requirements

Candidates must have a PhD in  Biochemistry, Biophysics or Structural
biology with strong skills in X-ray crystallography is required. Additional
skills in SAXS or EM, protein expression and purification are preferred.
This position will give the candidate exposure to many aspects of biologic
discovery and development.  Programming C++ or UNIX Shell Scripting is a
plus.

*BE VITAL in your career; be seen for the talent you bring to your work.
Explore opportunities within the Johnson & Johnson Family of Companies.*


Apply Here: http://www.Click2Apply.net/fc3m9w5

[ccp4bb] Ph.D. Position in Membrane Transport Research, Marburg, Germany

[Vasundara Srinivasan]

A DFG (German Research Foundation) funded Ph.D. position is available (starting 
immediately) at the Philipps-University of Marburg, Germany, to investigate the 
function of a mitochondrial ABC transporter, Atm1. The hitherto unidentified 
substrate exported by Atm1 is required for the assembly of Fe/S clusters in the 
cytosol and nucleus. Mutations in the atm1 gene have been shown to cause severe 
‘mitochondrial Fe overload’ and are associated with the disease X-linked 
sideroblastic anaemia in humans.

We have recently elucidated the crystal structure of Atm1 that provides an 
excellent platform for further studies (Srinivasan V. et al., Science. 2014 Mar 
7; 343(6175): 1137-40). Some of the most interesting and important aims are a) 
to elucidate the identity of the substrate and the mechanism of its export by 
Atm1, b) to establish the different conformational states involved in the 
transport mechanism, and c) to understand the relationship between mutation, 
biological structure and function and the disease state. To this end, the 
successful candidate will use a combination of powerful methods such as X-ray 
crystallography, cryo-electron microscopy and various techniques within 
biochemistry and cell biology.

Applications are invited from talented graduates who hold or expect to gain a 
Masters degree or equivalent in chemistry, biochemistry, physics, biophysics or 
related disciplines. Previous experience in a structural biology related 
pursuit is desirable but not essential. Good English language skills are 
essential; knowledge of German would be helpful but is not required.

 

The successful candidate will undertake a three-year Ph.D. studentship under 
the guidance of a team of structural and cell biologists. The student will have 
ample opportunities for data collection at ESRF, Grenoble, France, and the 
Swiss Light Source, Villigen, Switzerland.

Applications and informal project enquiries should be sent to Dr. Vasundara 
Srinivasan (vasundara.sriniva...@staff.uni-marburg.de). Applications should 
include a CV, a letter of motivation detailing research interests and 
expertise, and contact details for at least two referees and should be sent by 
email as a single pdf file.

Re: [ccp4bb] Residual density feature

[Colin Levy]

Dear all, 

Many thanks for the responses received,

To summarise the options for unidentified blobs appear to be:

1. Build something in and define it as a UNL (unknown ligand)

Some debate arose over the specifics of the term ³unknown ligand² and
wether a broader unknown entity description might be more accurate.

2. Leave the difference density and describe the location of the observed
feature using a SITE record.

As my intention was simply to draw attention to the presence of this
feature whilst not implying any identification I have chosen to go down
the latter route and simply leave the difference density for others to
ponder in the future.

Many thanks,

Colin




Manchester
Protein
Structure
Facility

Dr. Colin W. Levy
MIB G034
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk








On 16/06/2015 18:22, "Dale Tronrud"  wrote:

>-BEGIN PGP SIGNED MESSAGE-
>Hash: SHA1
>
>
>On 6/14/2015 2:49 AM, Robbie Joosten wrote:
>> Hi Colin,
>> 
>> You can define an UNL (unknown ligand) in the blob. This is the
>> standard name for such a compound. It becomes a bit messy in
>> refinement in terms of restraints, but it does exactly what you
>> want it to do: say you noticed the blob but couldn't figure out
>> what it was.
>> 
>   There is danger along this route - but I suppose this is a
>philosophical matter.  Your PDB file is your model for what is in the
>crystal.  If you don't know what a compound in your crystal is, can
>you say that you have modeled it?  What are your intentions when you
>place this "unknown" residue in your model -- Are you just placing a
>marker to tell those who follow that you noticed something here or are
>you saying "this is how electrons are arranged here".
>
>   Recently I was looking at 1I1W for some reason.  It is a very nice
>model at 0.89 A resolution.  It contains, however, several single atom
>residues of type UNX and the atoms are of type X.  The problem I have
>is that these atoms have their occupancy set to 1.0 and have varying B
>factors.  What am I supposed to make of a fully occupied atom of
>unknown type?
>
>   Apparently I'm not alone in my confusion.  The Electron Density
>Server does not supply a map for this entry.  I can see nothing wrong
>with the data nor the rest of the model so I presume the service is
>failing because it doesn't know how to calculate the scattering of an
>atom of unknown type.
>
>   So, my question is - If you place marker atoms to indicate the
>binding of any unknown ligand, should the difference density disappear
>from your map?  Certainly if you are interested in bootstrapping phase
>information you would want this, but is this appropriate for deposition?
>Should you be able to say your difference map is flat and your R value
>low when all you did was shrug your shoulders and say "I don't know"?
>
>   There is a, sadly underused, feature of the PDB format called the
>SITE record.  With it you can describe the residues of your protein
>that form a binding site and give a text description in a REMARK 800
>statement.  This option would allow you to acknowledge that something
>is binding at this location but leave the difference peak for others
>to view and puzzle over on their own.
>
>Dale Tronrud
>
>> Cheers, Robbie
>> 
>>> -Original Message- From: CCP4 bulletin board
>>> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent:
>>> Sunday, June 14, 2015 11:36 To: CCP4BB@JISCMAIL.AC.UK Subject:
>>> Re: [ccp4bb] Residual density feature
>>> 
>>> Dear Colin,
>>> 
>>> 
>>> 
>>> I believe people usually refer to it as "unidentified blob" when
>>> depositing/writing in
>> these
>>> cases. But I wonder whether others may suggest better options.
>>> 
>>> 
>>> 
>>> Best,
>>> 
>>> 
>>> 
>>> D
>>> 
>>>  From: CCP4 bulletin board
>>> [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Levy
>>> [c.l...@manchester.ac.uk] Sent: 14 June 2015 09:53 To: ccp4bb
>>> Subject: [ccp4bb] Residual density feature
>>> 
>>> Dear all,
>>> 
>>> I am currently working on a structure that contains a residual
>>> density feature located
>> within
>>> the active site. Due to a combination of factors including
>>> limited occupancy, modest resolution, twinning etc it has not
>>> been possible to unambiguously identify this feature
>> despite
>>> fairly extensive efforts.
>>> 
>>> What is the best way of dealing with such a feature when
>>> depositing the structure?
>> Ideally I
>>> would like to draw attention to the presence of residual density
>>> whilst not implying
>> that I have
>>> been able to identify it.
>>> 
>>> Many thanks,
>>> 
>>> Colin
>>> 
>>> 
>>> Manchester Protein Structure Facility
>>> 
>>> Dr. Colin W. Levy MIB G034 Tel.  0161 275 5090 Mob.07786 197 554
>>> c.l...@manchester.ac.uk
>>> 
>>> 
>>> -- This e-mail and any attachments may contain confidential,
>>> copyright and or privileged material, and are for the use of the
>>> intended addressee only. If you are not th

[ccp4bb] Post-doctoral positions at Indian Institute of Technology, Kanpur

[Arun Shukla]

Several post-doctoral positions are available in our laboratory to
work on cutting edge projects related to GPCR biology (determining
crystal structures, discovering new signaling pathways and generating
synthetic tools through combinatorial approaches). We are looking for
candidates with relevant experience (protein biochemistry & X-ray
crystallography). Please refer to Nat Rev Mol Cell Biol, 2015
Feb;16(2):69-81; Cell, 2014 Dec 18;159(7):1712; Trends Biochem Sci,
2014 Dec;39(12):594-602; Nature,  2014 Aug 14;512(7513):218-22;
Nature, 2013 May 2;497(7447):137-41 for a general overview of the
research direction and experimental approaches. These positions are
supported by the Wellcome Trust/DBT India Alliance, Department of
Science & Technology (DST, India) and Department of Biotechnology
(DBT, India). Interested applicants are requested to send their CV and
the name of three referees to arshu...@iitk.ac.in.