1v80

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{{Seed}}
 
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[[Image:1v80.png|left|200px]]
 
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==Solution structures of ubiquitin at 30 bar and 3 kbar==
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The line below this paragraph, containing "STRUCTURE_1v80", creates the "Structure Box" on the page.
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<StructureSection load='1v80' size='340' side='right'caption='[[1v80]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1v80]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V80 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V80 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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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=1v80 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v80 OCA], [https://pdbe.org/1v80 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v80 RCSB], [https://www.ebi.ac.uk/pdbsum/1v80 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v80 ProSAT], [https://www.topsan.org/Proteins/RSGI/1v80 TOPSAN]</span></td></tr>
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{{STRUCTURE_1v80| PDB=1v80 | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UBC_BOVIN UBC_BOVIN] Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
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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/v8/1v80_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1v80 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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Conformational fluctuation plays a key role in protein function, but we know little about the associated structural changes. Here we present a general method for elucidating, at the atomic level, a large-scale shape change of a protein molecule in solution undergoing conformational fluctuation. The method utilizes the intimate relationship between conformation and partial molar volume and determines three-dimensional structures of a protein at different pressures using variable pressure NMR technique, whereby NOE distance and torsion angle constraints are used to create average coordinates. Ubiquitin (pH 4.6 at 20 degrees C) was chosen as the first target, for which structures were determined at 30 bar and at 3 kbar, giving "NMR snapshots" of a fluctuating protein structure at atomic resolution. The result reveals that the helix swings in and out by &gt;3 angstroms with a simultaneous reorientation of the C-terminal segment, providing an "open" conformer suitable for enzyme recognition. Spin relaxation analysis indicates that this fluctuation occurs in the ten microsecond time range with activation volumes -4.2(+/-3.2) and 18.5(+/-3.0) ml/mol for the "closed-to-open" and the "open-to-closed" transitions, respectively.
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===Solution structures of ubiquitin at 30 bar and 3 kbar===
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NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.,Kitahara R, Yokoyama S, Akasaka K J Mol Biol. 2005 Mar 25;347(2):277-85. PMID:15740740<ref>PMID:15740740</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 1v80" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15740740}}, adds the Publication Abstract to the page
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*[[Ribosomal protein L40|Ribosomal protein L40]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15740740 is the PubMed ID number.
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*[[3D structures of ubiquitin|3D structures of ubiquitin]]
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== References ==
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{{ABSTRACT_PUBMED_15740740}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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1V80 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V80 OCA].
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==Reference==
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NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar., Kitahara R, Yokoyama S, Akasaka K, J Mol Biol. 2005 Mar 25;347(2):277-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15740740 15740740]
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[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Akasaka, K.]]
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[[Category: Large Structures]]
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[[Category: Kitahara, R.]]
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[[Category: Akasaka K]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Kitahara R]]
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[[Category: Yokoyama, S.]]
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[[Category: Yokoyama S]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Pressure]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Signaling protein]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 10:45:34 2008''
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Current revision

Solution structures of ubiquitin at 30 bar and 3 kbar

PDB ID 1v80

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