1m5q

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[[Image:1m5q.gif|left|200px]]
 
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{{Structure
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==Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum==
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|PDB= 1m5q |SIZE=350|CAPTION= <scene name='initialview01'>1m5q</scene>, resolution 2.00&Aring;
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<StructureSection load='1m5q' size='340' side='right'caption='[[1m5q]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> and <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene>
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<table><tr><td colspan='2'>[[1m5q]] is a 28 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=1M5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5Q FirstGlance]. <br>
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|ACTIVITY=
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</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&#8491;</td></tr>
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|GENE= SmAP3 gene (Pae2122) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 Pyrobaculum aerophilum])
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<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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5q OCA], [https://pdbe.org/1m5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5q RCSB], [https://www.ebi.ac.uk/pdbsum/1m5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5q ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8ZVU2_PYRAE Q8ZVU2_PYRAE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m5/1m5q_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1m5q ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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To better understand the roles of Sm proteins in forming the cores of many RNA-processing ribonucleoproteins, we determined the crystal structure of an atypical Sm-like archaeal protein (SmAP3) in which the conserved Sm domain is augmented by a previously uncharacterized, mixed alpha/beta C-terminal domain. The structure reveals an unexpected SmAP3 14-mer that is perforated by a cylindrical pore and is bound to 14 cadmium (Cd(2+)) ions. Individual heptamers adopt either "apical" or "equatorial" conformations that chelate Cd(2+) differently. SmAP3 forms supraheptameric oligomers (SmAP3)(n = 7,14,28) in solution, and assembly of the asymmetric 14-mer is modulated by differential divalent cation-binding in apical and equatorial subunits. Phylogenetic and sequence analyses substantiate SmAP3s as a unique subset of SmAPs. These results distinguish SmAP3s from other Sm proteins and provide a model for the structure and properties of Sm proteins &gt;100 residues in length, e.g., several human Sm proteins.
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'''Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum'''
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Structure and assembly of an augmented Sm-like archaeal protein 14-mer.,Mura C, Phillips M, Kozhukhovsky A, Eisenberg D Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4539-44. Epub 2003 Mar 31. PMID:12668760<ref>PMID:12668760</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1m5q" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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To better understand the roles of Sm proteins in forming the cores of many RNA-processing ribonucleoproteins, we determined the crystal structure of an atypical Sm-like archaeal protein (SmAP3) in which the conserved Sm domain is augmented by a previously uncharacterized, mixed alpha/beta C-terminal domain. The structure reveals an unexpected SmAP3 14-mer that is perforated by a cylindrical pore and is bound to 14 cadmium (Cd(2+)) ions. Individual heptamers adopt either "apical" or "equatorial" conformations that chelate Cd(2+) differently. SmAP3 forms supraheptameric oligomers (SmAP3)(n = 7,14,28) in solution, and assembly of the asymmetric 14-mer is modulated by differential divalent cation-binding in apical and equatorial subunits. Phylogenetic and sequence analyses substantiate SmAP3s as a unique subset of SmAPs. These results distinguish SmAP3s from other Sm proteins and provide a model for the structure and properties of Sm proteins &gt;100 residues in length, e.g., several human Sm proteins.
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*[[Sm-like protein 3D structures|Sm-like protein 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1M5Q 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=1M5Q OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Structure and assembly of an augmented Sm-like archaeal protein 14-mer., Mura C, Phillips M, Kozhukhovsky A, Eisenberg D, Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4539-44. Epub 2003 Mar 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12668760 12668760]
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[[Category: Pyrobaculum aerophilum]]
[[Category: Pyrobaculum aerophilum]]
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[[Category: Single protein]]
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[[Category: Eisenberg D]]
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[[Category: Eisenberg, D.]]
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[[Category: Kozhukhovsky A]]
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[[Category: Kozhukhovsky, A.]]
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[[Category: Mura C]]
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[[Category: Mura, C.]]
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[[Category: Phillips M]]
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[[Category: Phillips, M.]]
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[[Category: ACY]]
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[[Category: CD]]
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[[Category: GOL]]
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[[Category: NA]]
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[[Category: 14-mer]]
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[[Category: b-sheet toroid]]
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[[Category: cadmium-binding site]]
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[[Category: ob-like fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:39:13 2008''
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Current revision

Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum

PDB ID 1m5q

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