1ryq: Difference between revisions

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New page: left|200px<br /><applet load="1ryq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ryq, resolution 1.38Å" /> '''Putative DNA-directe...
 
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[[Image:1ryq.jpg|left|200px]]<br /><applet load="1ryq" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ryq, resolution 1.38&Aring;" />
'''Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001'''<br />


==Overview==
==Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001==
The determination of protein structures on a genomic scale requires both, computing capacity and efficiency increases at many stages along the, complex process. By combining bioinformatics workflow-management, techniques, cluster-based computing and popular crystallographic, structure-determination software packages, an efficient and powerful new, tool for structural biology/genomics has been developed. Using the, workflow manager and a simple web interface, the researcher can, in a few, easy steps, set up hundreds of structure-determination jobs, each using a, slightly different set of program input parameters, thus efficiently, screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure, determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web, interface. This approach has been applied with success in more than 30, cases. Examples of successful structure determinations based on, single-wavelength scattering (SAS) are described and include cases where, the 'rational' crystallographer-based selection of input parameters values, had failed.
<StructureSection load='1ryq' size='340' side='right'caption='[[1ryq]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ryq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYQ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.38&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ryq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryq OCA], [https://pdbe.org/1ryq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ryq RCSB], [https://www.ebi.ac.uk/pdbsum/1ryq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ryq ProSAT], [https://www.topsan.org/Proteins/SECSG/1ryq TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SPT4_PYRFU SPT4_PYRFU] Stimulates transcription elongation.<ref>PMID:21386817</ref> <ref>PMID:21187417</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ry/1ryq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ryq ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1RYQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RYQ OCA].
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 
== References ==
==Reference==
<references/>
Parameter-space screening: a powerful tool for high-throughput crystal structure determination., Liu ZJ, Lin D, Tempel W, Praissman JL, Rose JP, Wang BC, Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. Epub 2005, Apr 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15858261 15858261]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Single protein]]
[[Category: Adams MWW]]
[[Category: Adams, M.W.W.]]
[[Category: Arendall III WB]]
[[Category: Brereton, P.S.]]
[[Category: Brereton PS]]
[[Category: Chen, L.]]
[[Category: Chen L]]
[[Category: II, F.L.Poole.]]
[[Category: Izumi M]]
[[Category: III, W.B.Arendall.]]
[[Category: Jenney Jr FE]]
[[Category: Izumi, M.]]
[[Category: Lee HS]]
[[Category: Jr., F.E.Jenney.]]
[[Category: Liu Z-J]]
[[Category: Lee, H.S.]]
[[Category: Poole II FL]]
[[Category: Liu, Z.J.]]
[[Category: Richardson DC]]
[[Category: Richardson, D.C.]]
[[Category: Richardson JS]]
[[Category: Richardson, J.S.]]
[[Category: Rose JP]]
[[Category: Rose, J.P.]]
[[Category: Shah A]]
[[Category: SECSG, Southeast.Collaboratory.for.Structural.Genomics.]]
[[Category: Shah C]]
[[Category: Shah, A.]]
[[Category: Sugar FJ]]
[[Category: Shah, C.]]
[[Category: Tempel W]]
[[Category: Sugar, F.J.]]
[[Category: Wang B-C]]
[[Category: Tempel, W.]]
[[Category: Wang, B.C.]]
[[Category: ZN]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: rna polymerase]]
[[Category: secsg]]
[[Category: southeast collaboratory for structural genomics]]
[[Category: structural genomics]]
[[Category: zinc]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:31:49 2007''

Latest revision as of 11:26, 14 February 2024

Putative DNA-directed RNA polymerase, subunit e from Pyrococcus Furiosus Pfu-263306-001Putative DNA-directed RNA polymerase, subunit e from Pyrococcus Furiosus Pfu-263306-001

Structural highlights

1ryq is a 1 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.38Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SPT4_PYRFU Stimulates transcription elongation.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Martinez-Rucobo FW, Sainsbury S, Cheung AC, Cramer P. Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J. 2011 Mar 8. PMID:21386817 doi:10.1038/emboj.2011.64
  2. ↑ Klein BJ, Bose D, Baker KJ, Yusoff ZM, Zhang X, Murakami KS. RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):546-50. Epub 2010 Dec 27. PMID:21187417 doi:10.1073/pnas.1013828108

1ryq, resolution 1.38Å

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