Crystal structure of the polymerase PAC�PB1N complex from an avian influenza H5N1 virus

I don't find section about polymerases

where is it ?

http://www.eurekalert.org/pub_releases/2008-07/dnl-nd071508.php
Public release date: 15-Jul-2008

Contact: Steve McGregor
smcgregor@anl.gov
630-252-5580
DOE/Argonne National Laboratory (http://www.anl.gov/)
Newly described 'dragon' protein could be key to bird flu cure

ARGONNE, Ill. (July 15, 2008) -- Scientists and researchers have taken a big step closer to a cure for the most common strain of avian influenza, or "bird flu," the potential pandemic that has claimed more than 200 lives and infected nearly 400 people in 14 countries since it was identified in 2003.
Researchers at the U.S. Department of Energy's (DOE) Argonne National Laboratory, in conjunction with scientists from China and Singapore, have crystallized and characterized the structure of one of the most important protein complexes of the H5N1 virus, the most common strain of bird flu.
All viruses, including H5N1, contain only a small number of proteins that govern all of the viruses' functions. In H5N1, perhaps the most important of these proteins is RNA polymerase, which contains the instructions that allows the virus to copy itself along with all of its genetic material. The Argonne study focused on H5N1's RNA polymerase protein, which contains three subunits: PA, PB1 and PB2.
After performing X-ray crystallography on the protein crystals at Argonne's Structural Biology Center 19ID beamline at the Advanced Photon Source, the researchers saw a surprising resemblance in the protein structure's image. "When we mapped out the PA subunit, it looked very much like the head of a dragon," said Argonne biophysicist Andrzej Joachimiak. "One domain looked like the dragon's brains, and the other looked like its mouth."
During RNA replication – the phase during which the virus "reproduces" – all three of the subunits of the protein assemble themselves in a particular configuration. In order for this congregation to take place, the researchers determined the end of the PB1 subunit has to insert itself and bind to the "dragon's mouth" part of the PA subunit.
This unexpected relationship between the two subunits could inspire a number of different therapies or vaccines for H5N1 that rely on muzzling the "dragon's" jaws with another molecule or chemical compound that would block the PB1 subunit's access to the PA site, according to Joachimiak. "If we can put a bit in the dragon's mouth, we can slow or even potentially someday stop the spread of avian flu," he said. "Since we are talking about a relatively small protein surface area, finding a way to inhibit RNA replication in H5N1 seems very feasible."
Joachimiak hopes to more precisely identify the types of compounds that could inhibit RNA replication in H5N1 by looking at the atomic-level grooves and pockets within the PA "mouth" region. According to Joachimiak, scientists must gain a more thorough understanding of the geometry of that small region in order to effectively synthesize drugs that could prevent the further spread of bird flu.
###
Argonne researchers Joachimiak and Rongguang Zhang collaborated with Zihe Rao and Yingfang Liu, both members of the Institute of Biophysics of Chinese Academy of Sciences. Rao is one of the most influential Chinese crystallographers and biophysicists, Joachimiak said. The protein samples were manufactured in China and crystals were shipped to Argonne for data collection and structural analysis.
The results of the study will be reported in an upcoming issue of Nature and can be found online at http://dx.doi.org/10.1038/nature07120. The work was funded by the National Natural Science Foundation of China as well as the Chinese Ministry of Science and Technology and the U.S. Department of Energy's Office of Biological and Environmental Research.
About Argonne
The U.S. Department of Energy's Argonne National Laboratory brings the world's brightest scientists and engineers together to find exciting and creative new solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50

Letter

Nature advance online publication 9 July 2008 doi:10.1038/nature07120; Received 25 March 2008; Accepted 23 May 2008; Published online 9 July 2008
Crystal structure of the polymerase PA_C–PB1_N complex from an avian influenza H5N1 virus

Xiaojing He^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)}, Jie Zhou^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)}, Mark Bartlam^{2 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a2)}, Rongguang Zhang^{3 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a3)}, Jianyuan Ma^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)}, Zhiyong Lou^{4 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a4)}, Xuemei Li^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1),}^{4 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a4)}, Jingjing Li^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)}, Andrzej Joachimiak^{3 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a3)}, Zonghao Zeng^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)}, Ruowen Ge^{5 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a5)}, Zihe Rao^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1),}^{2 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a2),}^{4 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a4)} & Yingfang Liu^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)}
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
College of Life Sciences and Tianjin State Laboratory of Protein Sciences, Nankai University, Tianjin 300071, China
Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
Department of Biological Sciences, National University of Singapore, 117543 SingaporeCorrespondence to: Zihe Rao^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1),}^{2 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a2),}^{4 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a4)}Yingfang Liu^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#a1)} Correspondence and requests for materials should be addressed to Z.R. (Email: raozh@xtal.tsinghua.edu.cn) or Y.L. (Email: liuy@ibp.ac.cn).

Top of page (http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07120.html;jsessionid=46598356F0F97E619B4427 62F0473F50#top)The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health^{1 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B1)}. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs^{2 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B2)}. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding^{3, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B3)}^{4 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B4)}; PA is implicated in RNA replication^{5, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B5)}^{6, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B6)}^{7, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B7)}^{8, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B8)}^{9, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B9)}^{10 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B10)} and proteolytic activity^{11, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B11)}^{12, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B12)}^{13, (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B13)}^{14 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B14)}, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PA_C, residues 257–716) in complex with the PA-binding region of PB1 (PB1_N, residues 1–25). PA_C has a fold resembling a dragon's head with PB1_N clamped into its open 'jaws'. PB1_N is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1_N to PA_C at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA_C with the http://www.nature.com/__chars/lambda/black/med/base/glyph.gif3 reovirus polymerase structure, and docking the PA_C structure into an available low resolution electron microscopy map.

8 PB2
8 PB1
8 PA

correct
I must read the article you ve found

thank you for this links..with " 3D " pictures.

http://nar.oxfordjournals.org/cgi/content/full/gkm336v1/F4

do someone know crystallography and if it is a reliable method ?

Standard method of determining 3D structure. The tricky bit is to get good crystals. X-ray diffraction patterns are then analysed to calculate the structure that would have generated the pattern. X-rays are used as their wavelength is about right to cause diffraction on the Angstrom scales of atomic arrangements.

done :)
.

do some one have the ability to move this tread at
http://www.flutrackers.com/forum/forumdisplay.php?f=1432

thanks :)

what section do you mean ?

I have not enough phantasy to see the dragon here:
http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature07120_F1.html#figure-title

number of copies of that protein inside one virus

remembering this thread:
http://www.singtomeohmuse.com/viewtopic.php?t=2134
-----edit1--------
also this one:
http://flutrackers.com/forum/showthread.php?t=50277
copied from:
http://www.newfluwiki2.com/showDiary.do?diaryId=2076
------------------

so about 5 PB2,5 PB1,5 PA and 125 NP form one RNP to surround
and protect one of the 8 RNAs

hmm, looks strange, I will have to check

http://nar.oxfordjournals.org/cgi/content/full/gkm336v1/F4
http://nar.oxfordjournals.org/cgi/content/full/gkm336v1/F5

I can't quickly find where are the 30-60 PB2s, 30-60PB1s,30-60PAs,1000NPs
in the virus.
I get:
9*8=72 NPs
8 PB2s
8 PB1s
8 PAs

for example : a section where all articles about polymerases are stored.. did'nt we have that ?

I have no imagination or I have problems with my eyes , I dont see a dragon, nor a dragon mouth..
Most of the autors are chinese : it s easier for them to see dragon..they re trained. :)

here ?
a mouth ?
http://www.nature.com/nature/journal/vaop/ncurrent/images/nature07120-f2.2.jpg
a, An enlarged view of the PA_C groove and channel, rotated by 90° about the x axis relative to Fig. 1a (http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature07120_F1.html) and with the same colouring scheme. The extended N-terminal loop from residues 257–288 is coloured pale green. Conserved residues lining the groove and channel are shown in stick representation and labelled. b, A surface representation of the same region of PA_C coloured by electrostatic charge from red (-10 k_bT/e_c) to blue (+10 k_bT/e_c), where k_bis the Boltzmann constant, T is temperature and e_cis the electron charge. Residues lining the highly basic groove are labelled. c, Location of known mutations in the PA_C structure. PA_C and PB1_N are shown in ribbon representation and coloured according to the scheme in Fig. 1 (http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature07120_F1.html). d, Interaction between PA_C and PB1_N. PA_C and PB1_N are shown in ribbon representation and coloured according to the scheme in Fig. 1 (http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature07120_F1.html). Residues interacting with the PB1_N peptide are shown in stick representation and labelled. e, In vitro binding assay for PB1_N to the W706A/Q670A PA_C double mutant. WTPA_C, wild-type PA_C.

http://www.nature.com/nature/journal/vaop/ncurrent/images/nature07120-f3.2.jpghttp://www.nature.com/nature/journal/vaop/ncurrent/images/nature07120-f3.2.jpg

a, Model of the influenza polymerase heterotrimer constructed using the http://www.nature.com/__chars/lambda/black/med/base/glyph.gif3 reovirus polymerase structure^{22 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B22)}. PA_C is coloured blue, PB1_N is magenta, http://www.nature.com/__chars/lambda/black/med/base/glyph.gif3 domain II is red and the http://www.nature.com/__chars/lambda/black/med/base/glyph.gif3 domain III is in green. b, Putative arrangement of PA, PB1 and PB2 in the influenza polymerase heterotrimer. Colouring is the same as in a, with PB1 in red and PB2 in green. c, d, PA_C docked into the electron microscopy map of the isolated heterotrimer^{24 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07120.html#B24)}. PA_C is shown in ribbon representation and in blue. Putative locations of the PB1 and PB2 proteins are shown in red and green, respectively.

thank you Mixin, I had seen the mouth or chanel, but not the brain ...

do someone know crystallography and if it is a reliable method ?

Gsgs , what do you think with : ( what does it mean )

30-60 PB2s per virus
30-60 PB1s per virus
30-60 PAs per virus
1000 NPs per virus

gsgs : 8x9 Np : it is exact.
I ve read again the pdf from Nancy Cox and Kawaoka

JJackson, thank you for your answer.

the article find by gsgs is to technical for me, but they give a 3 D picture of polymerase alone and bound to NP.

http://nar.oxfordjournals.org/content/vol0/issue2007/images/medium/gkm336f5.gif

Figure 5. Fitting between soluble and RNP-associated polymerase. (A) Fitting between the 3D reconstructions of the soluble (blue transparency) and the RNP-bound (pink solid density) polymerase, which are shown over-imposed. (B) Locations of the subunits in the soluble polymerase denoted as a result of its comparison with the model for the polymerase bound to the RNP (15) where these were mapped by antibody labelling. (C) Chimeric model using the 3D structures of an RNP (15) and of the soluble polymerase. The backside of the polymerase (blue) contains the sites of the interaction with the NP monomers whereas the front side (green) is opposite to the NP ring (15).

ahh, section at FT. (not at PB1 or such)
I think there is no section for polymerase here
You can copy the nice pictures to the picture room.
Maybe someone can spot the dragon.

so, PB1_N [507ff,537ff] connects to PA_C [442ff,638ff]

we often have reassortment of PB1 alone, not together with PA.
So different mouths fit well to different brains ?

just recalling for my understanding:

So we are entirely on the protein-level here (RNPs)
and synonymous mutations play no role

30-60 PB2s per virus
30-60 PB1s per virus
30-60 PAs per virus
1000 NPs per virus

forming the 8 RNP-complexes that surround and protect
the 8 RNA segments

-------------
These segments are associated with nucleoprotein and three polymerase subunits, designated PA, PB1 and PB2; the resultant ribonucleoprotein complexes (RNPs) resemble a twisted rod (10–15 nm in width and 30–120 nm in length) that is folded back and coiled on itself2, 3, 4. Late in viral infection, newly synthesized RNPs are transported from the nucleus to the plasma membrane, where they are incorporated into progeny virions capable of infecting other cells

Pitcure B:
K539 is the dragon's mouth and the round(ish) area to the left is its brain.

#If you have any other info about this subject , Please add it free.#

March 21st, 2010, posted by smith

hznq.com edit

hznq.com
welcome to my space