1lnx: Difference between revisions

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-[[Image:1lnx.gif|left|200px]]
- {{Structure
+==Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)==
-|PDB= 1lnx |SIZE=350|CAPTION= <scene name='initialview01'>1lnx</scene>, resolution 2.05&Aring;
+<StructureSection load='1lnx' size='340' side='right'caption='[[1lnx]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene>
+<table><tr><td colspan='2'>[[1lnx]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LNX FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-|GENE= SmAP1, GPA2549 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 Pyrobaculum aerophilum])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnx OCA], [https://pdbe.org/1lnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lnx RCSB], [https://www.ebi.ac.uk/pdbsum/1lnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lnx ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1i4k|1I4K]], [[1i5l|1I5L]], [[1i8f|1I8F]], [[1i81|1I81]], [[1jbm|1JBM]], [[1jri|1JRI]], [[1loj|1LOJ]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnx OCA], [http://www.ebi.ac.uk/pdbsum/1lnx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1lnx RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/Q8ZYG5_PYRAE Q8ZYG5_PYRAE]
+== 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/ln/1lnx_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=1lnx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth). Ultracentrifugation shows that Mth SmAP1 is exclusively heptameric in solution, whereas Pae SmAP1 forms either disulfide-bonded 14-mers or sub-heptameric states (depending on the redox potential). By electron microscopy, we show that Pae and Mth SmAP1 polymerize into bundles of well ordered fibers that probably form by head-to-tail stacking of heptamers. The crystallographic results reported here corroborate these findings by showing heptamers and 14-mers of both Mth and Pae SmAP1 in four new crystal forms. The 1.9 A-resolution structure of Mth SmAP1 bound to uridine-5'-monophosphate (UMP) reveals conserved ligand-binding sites. The likely RNA binding site in Mth agrees with that determined for Archaeoglobus fulgidus (Afu) SmAP1. Finally, we found that both Pae and Mth SmAP1 gel-shift negatively supercoiled DNA. These results distinguish SmAPs from eukaryotic Sm proteins and suggest that SmAPs have a generic single-stranded nucleic acid-binding activity.
-'''Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)'''
+The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs).,Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D Protein Sci. 2003 Apr;12(4):832-47. PMID:12649441<ref>PMID:12649441</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1lnx" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth). Ultracentrifugation shows that Mth SmAP1 is exclusively heptameric in solution, whereas Pae SmAP1 forms either disulfide-bonded 14-mers or sub-heptameric states (depending on the redox potential). By electron microscopy, we show that Pae and Mth SmAP1 polymerize into bundles of well ordered fibers that probably form by head-to-tail stacking of heptamers. The crystallographic results reported here corroborate these findings by showing heptamers and 14-mers of both Mth and Pae SmAP1 in four new crystal forms. The 1.9 A-resolution structure of Mth SmAP1 bound to uridine-5'-monophosphate (UMP) reveals conserved ligand-binding sites. The likely RNA binding site in Mth agrees with that determined for Archaeoglobus fulgidus (Afu) SmAP1. Finally, we found that both Pae and Mth SmAP1 gel-shift negatively supercoiled DNA. These results distinguish SmAPs from eukaryotic Sm proteins and suggest that SmAPs have a generic single-stranded nucleic acid-binding activity.
+*[[Sm-like protein|Sm-like protein]]
+== References ==
-==About this Structure==
+<references/>
-LNX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNX OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs)., Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D, Protein Sci. 2003 Apr;12(4):832-47. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12649441 12649441]
 [[Category: Pyrobaculum aerophilum]]
-[[Category: Single protein]]
+[[Category: Eisenberg D]]
-[[Category: Eisenberg, D.]]
+[[Category: Kozhukhovsky A]]
-[[Category: Kozhukhovsky, A.]]
+[[Category: Mura C]]
-[[Category: Mura, C.]]
-[[Category: beta barrel-like structure (ob fold)]]
-[[Category: homoheptameric]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:05:03 2008''