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3ai5

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{{Seed}}
 
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[[Image:3ai5.png|left|200px]]
 
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==Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein==
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The line below this paragraph, containing "STRUCTURE_3ai5", creates the "Structure Box" on the page.
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<StructureSection load='3ai5' size='340' side='right'caption='[[3ai5]], [[Resolution|resolution]] 1.40&Aring;' 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'>[[3ai5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AI5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AI5 FirstGlance]. <br>
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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]] 1.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
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{{STRUCTURE_3ai5| PDB=3ai5 | SCENE= }}
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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=3ai5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ai5 OCA], [https://pdbe.org/3ai5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ai5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ai5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ai5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL40_MOUSE RL40_MOUSE] 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 proteotoxic stress response and cell cycle; 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.<ref>PMID:19754430</ref> Component of the 60S subunit of the ribosome.<ref>PMID:19754430</ref> <ref>PMID:36517592</ref> [https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
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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/ai/3ai5_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=3ai5 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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The generation of crystal lattice contacts by proteinaceous tags fused to target proteins is an attractive approach to aid in the crystallization of otherwise intractable proteins. Here, the use of green fluorescent protein (GFP) fusions for this purpose is demonstrated, using ubiquitin and the ubiquitin-binding motif (UBM) of Y-family polymerase iota as examples. The structure of the GFP-ubiquitin fusion protein revealed that the crystal lattice was formed by GFP moieties. Ubiquitin was accommodated in the lattice through interactions with the peripheral loops of GFP. However, in the GFP-UBM fusion crystal UBM formed extensive interactions with GFP and these interactions, together with UBM dimerization, mediated the crystal packing. Interestingly, the tyrosine residues that are involved in mediating crystal contacts in both GFP-ubiquitin and GFP-UBM crystals are arranged in a belt on the surface of the beta-barrel structure of GFP. Therefore, it is likely that GFP can assist in the crystallization of small proteins and of protein domains in general.
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===Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein===
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Crystallization of small proteins assisted by green fluorescent protein.,Suzuki N, Hiraki M, Yamada Y, Matsugaki N, Igarashi N, Kato R, Dikic I, Drew D, Iwata S, Wakatsuki S, Kawasaki M Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1059-66. Epub 2010, Sep 18. PMID:20944239<ref>PMID:20944239</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 3ai5" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20944239}}, adds the Publication Abstract to the page
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*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20944239 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20944239}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Aequorea victoria]]
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3AI5 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria,_mus_musculus Aequorea victoria, mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AI5 OCA].
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[[Category: Large Structures]]
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[[Category: Mus musculus]]
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==Reference==
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[[Category: Kawasaki M]]
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<ref group="xtra">PMID:20944239</ref><references group="xtra"/>
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[[Category: Suzuki N]]
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[[Category: Aequorea victoria, mus musculus]]
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[[Category: Wakatsuki S]]
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[[Category: Kawasaki, M.]]
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[[Category: Suzuki, N.]]
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[[Category: Wakatsuki, S.]]
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[[Category: Fluorescent protein]]
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[[Category: Fusion protein]]
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[[Category: Green fluorescent protein]]
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[[Category: Transcription]]
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[[Category: Ubiquitin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 11:37:12 2010''
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Current revision

Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein

PDB ID 3ai5

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