1ljo - Revision history

OCA at 07:33, 14 February 2024

2024-02-14T07:33:39Z

←Older revision		Revision as of 07:33, 14 February 2024
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	<StructureSection load='1ljo' size='340' side='right'caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1ljo' size='340' side='right'caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arcfl Arcfl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1LJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
-	</td></tr><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=CD:CADMIUM+ION'>CD</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.95Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]~~</~~div~~><~~/td></tr>~~	+	<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=CD:CADMIUM+ION'>CD</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])~~</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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [https://pdbe.org/1ljo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [https://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [~~http~~://pdbe.org/1ljo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O29885_ARCFU O29885_ARCFU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1ljo ConSurf].		</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=1ljo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Proteins of largely unknown function related to the Sm proteins present in the core domain of eukaryotic small nuclear ribonucleoprotein particles have recently been detected in Archaea. In contrast to eukaryotes, Archaea contain maximally two distinct Sm-related proteins belonging to different subfamilies, we refer to as Sm1 and Sm2. Here we report the crystal structures of the Sm1- and Sm2-type proteins from the hyperthermophilic euryarchaeon Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) at a resolution of 2.5 and 1.95 A, respectively. While the AF-Sm1 protein forms a heptameric ring structure similar to that found in other archaeal Sm1-type proteins, the AF-Sm2 protein unexpectedly forms a homo-hexamer in the crystals, and, as is evident from the mass spectrometric analysis, also in solution. Both proteins have essentially the same monomer fold and inter-subunit beta-sheet hydrogen bonding giving rise to a similar overall architecture of the doughnut-shaped six and seven-membered rings. In addition, a conserved uracil-binding pocket identified previously in an AF-Sm1/RNA complex, suggests a common RNA-binding mode for the AF-Sm1 and AF-Sm2 proteins, in line with solution studies showing preferential binding to U-rich oligonucleotides for both proteins. Clear differences are however seen in the charge distribution within the two structures. The rough faces of the rings, i.e. the faces not containing the base binding pockets, have opposite charges in the two structures, being predominantly positive in AF-Sm1 and negative in AF-Sm2. Differences in the ionic interactions between subunits provide an explanation for the distinctly different oligomerisation behaviour of the AF-Sm1 and AF-Sm2 proteins and of Sm1- and Sm2-type proteins in general, as well as the stability of their complexes. Implications for the functions of archaeal Sm proteins are being discussed.
-
-	Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus.,Toro I, Basquin J, Teo-Dreher H, Suck D J Mol Biol. 2002 Jun 28;320(1):129-42. PMID:12079339<ref>PMID:12079339</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ljo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Sm-like protein\|Sm-like protein]]	+	*[[Sm-like protein 3D structures\|Sm-like protein 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arcfl~~]]	+	[[Category: Archaeoglobus fulgidus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basquin, J]]	+	[[Category: Basquin J]]
-	[[Category: Suck, D]]	+	[[Category: Suck D]]
-	[[Category: Teo-Dreher, H]]	+	[[Category: Teo-Dreher H]]
-	[[Category: Toro, I]]	+	[[Category: Toro I]]
-	~~[[Category: Core snrnp domain]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Sm]]~~	+
-	~~[[Category: Snrnp]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 07:59, 25 November 2020

2020-11-25T07:59:15Z

←Older revision		Revision as of 07:59, 25 November 2020
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	==CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION==		==CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION==
-	<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='1ljo' size='340' side='right'caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>	+	</td></tr><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=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/1ljo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/1ljo_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1ljo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ljo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sm-like protein\|Sm-like protein]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Arcfl]]		[[Category: Arcfl]]
		+	[[Category: Large Structures]]
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
	[[Category: Suck, D]]		[[Category: Suck, D]]

OCA at 09:49, 12 October 2017

2017-10-12T09:49:50Z

←Older revision		Revision as of 09:49, 12 October 2017
Line 3:		Line 3:
	<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 1ljo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ljo" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Sm-like protein\|Sm-like protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arcfl]]
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
	[[Category: Suck, D]]		[[Category: Suck, D]]

OCA at 06:55, 5 April 2017

2017-04-05T06:55:32Z

←Older revision		Revision as of 06:55, 5 April 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION==		==CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION==
	<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljo ProSAT]</span></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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arcfl]]
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
	[[Category: Suck, D]]		[[Category: Suck, D]]

OCA at 19:45, 7 February 2016

2016-02-07T19:45:11Z

←Older revision		Revision as of 19:45, 7 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1ljo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:27, 10 September 2015

2015-09-10T04:27:29Z

←Older revision		Revision as of 04:27, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus Archaeoglobus fulgidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ~~Archaeoglobus fulgidus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum]</span></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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://pdbe.org/1ljo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1ljo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Archaeoglobus fulgidus~~]]	+	[[Category: Arcfl]]
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
	[[Category: Suck, D]]		[[Category: Suck, D]]

OCA at 16:09, 5 January 2015

2015-01-05T16:09:05Z

←Older revision		Revision as of 16:09, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum]</span></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=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
-	[[Category: Basquin, J.]]	+	[[Category: Basquin, J]]
-	[[Category: Suck, D.]]	+	[[Category: Suck, D]]
-	[[Category: Teo-Dreher, H.]]	+	[[Category: Teo-Dreher, H]]
-	[[Category: Toro, I.]]	+	[[Category: Toro, I]]
	[[Category: Core snrnp domain]]		[[Category: Core snrnp domain]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]

OCA at 13:30, 28 September 2014

2014-09-28T13:30:31Z

←Older revision		Revision as of 13:30, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ljo.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION==
		+	<StructureSection load='1ljo' size='340' side='right' caption='[[1ljo]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3b\|1d3b]], [[1b34\|1b34]], [[1i81\|1i81]], [[1i8f\|1i8f]], [[1i5l\|1i5l]], [[1i4k\|1i4k]], [[1jri\|1jri]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF0362 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ljo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ljo RCSB], [http://www.ebi.ac.uk/pdbsum/1ljo PDBsum]</span></td></tr>
		+	<table>
		+	== 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/lj/1ljo_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteins of largely unknown function related to the Sm proteins present in the core domain of eukaryotic small nuclear ribonucleoprotein particles have recently been detected in Archaea. In contrast to eukaryotes, Archaea contain maximally two distinct Sm-related proteins belonging to different subfamilies, we refer to as Sm1 and Sm2. Here we report the crystal structures of the Sm1- and Sm2-type proteins from the hyperthermophilic euryarchaeon Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) at a resolution of 2.5 and 1.95 A, respectively. While the AF-Sm1 protein forms a heptameric ring structure similar to that found in other archaeal Sm1-type proteins, the AF-Sm2 protein unexpectedly forms a homo-hexamer in the crystals, and, as is evident from the mass spectrometric analysis, also in solution. Both proteins have essentially the same monomer fold and inter-subunit beta-sheet hydrogen bonding giving rise to a similar overall architecture of the doughnut-shaped six and seven-membered rings. In addition, a conserved uracil-binding pocket identified previously in an AF-Sm1/RNA complex, suggests a common RNA-binding mode for the AF-Sm1 and AF-Sm2 proteins, in line with solution studies showing preferential binding to U-rich oligonucleotides for both proteins. Clear differences are however seen in the charge distribution within the two structures. The rough faces of the rings, i.e. the faces not containing the base binding pockets, have opposite charges in the two structures, being predominantly positive in AF-Sm1 and negative in AF-Sm2. Differences in the ionic interactions between subunits provide an explanation for the distinctly different oligomerisation behaviour of the AF-Sm1 and AF-Sm2 proteins and of Sm1- and Sm2-type proteins in general, as well as the stability of their complexes. Implications for the functions of archaeal Sm proteins are being discussed.

-	~~{{STRUCTURE_1ljo\| PDB=1ljo \| SCENE= }}~~	+	Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus.,Toro I, Basquin J, Teo-Dreher H, Suck D J Mol Biol. 2002 Jun 28;320(1):129-42. PMID:12079339<ref>PMID:12079339</ref>

-	~~===CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12079339}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ljo]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA].~~	+

	==See Also==		==See Also==
	*[[Sm-like protein\|Sm-like protein]]		*[[Sm-like protein\|Sm-like protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012079339<~~/~~ref~~><~~ref group="xtra">PMID:011970895</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Basquin, J.]]		[[Category: Basquin, J.]]

OCA: Protected "1ljo" [edit=sysop:move=sysop]

2012-12-05T20:23:12Z

Protected "1ljo" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:23, 5 December 2012

OCA at 20:23, 5 December 2012

2012-12-05T20:23:10Z

←Older revision		Revision as of 20:23, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1ljo.png\|left\|200px]]		[[Image:1ljo.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ljo", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1ljo\| PDB=1ljo \| SCENE= }}		{{STRUCTURE_1ljo\| PDB=1ljo \| SCENE= }}

	===CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION===		===CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12079339}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12079339 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12079339}}		{{ABSTRACT_PUBMED_12079339}}

	==About this Structure==		==About this Structure==
-	~~1LJO~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA].	+	[[1ljo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJO OCA].
		+
		+	==See Also==
		+	*[[Sm-like protein\|Sm-like protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12079339~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012079339</ref><ref group="xtra">PMID:011970895</ref><references group="xtra"/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Basquin, J.]]		[[Category: Basquin, J.]]
Line 33:		Line 24:
	[[Category: Sm]]		[[Category: Sm]]
	[[Category: Snrnp]]		[[Category: Snrnp]]
-		+	[[Category: Unknown function]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 16:05:35 2009''~~	+