1ryq

From Proteopedia

(Difference between revisions)

Revision as of 09:00, 21 April 2021

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

Structural highlights

1ryq is a 1 chain structure with sequence from Atcc 43587. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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.

Publication Abstract from PubMed

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.

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:15858261^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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
↑ Liu ZJ, Lin D, Tempel W, Praissman JL, Rose JP, Wang BC. Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. Epub 2005, Apr 20. PMID:15858261 doi:10.1107/S0907444905003239

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ryq"

@@ Line 3: / Line 3: @@
 <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 [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RYQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ryq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ryq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryq OCA], [http://pdbe.org/1ryq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ryq RCSB], [http://www.ebi.ac.uk/pdbsum/1ryq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ryq ProSAT], [http://www.topsan.org/Proteins/SECSG/1ryq TOPSAN]</span></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 ==
-[[http://www.uniprot.org/uniprot/SPT4_PYRFU SPT4_PYRFU]] Stimulates transcription elongation.<ref>PMID:21386817</ref> <ref>PMID:21187417</ref>
+[[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]]
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 == References ==
 <references/>

1ryq

From Proteopedia

Revision as of 09:00, 21 April 2021

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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