3vdz

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Current revision (10:35, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3vdz' size='340' side='right'caption='[[3vdz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='3vdz' size='340' side='right'caption='[[3vdz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vdz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VDZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vdz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VDZ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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]] 2.4&#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=GD:GADOLINIUM+ATOM'>GD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3vdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdz OCA], [https://pdbe.org/3vdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdz RCSB], [https://www.ebi.ac.uk/pdbsum/3vdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdz ProSAT]</span></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=3vdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdz OCA], [https://pdbe.org/3vdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdz RCSB], [https://www.ebi.ac.uk/pdbsum/3vdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdz ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_HUMAN] 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.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
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Lanthanide-binding tags (LBTs), peptide-based coexpression tags with high affinity for lanthanide ions, have previously been applied as luminescent probes to provide phasing for structure determination in X-ray crystallography and to provide restraints for structural refinement and distance information in NMR. The native affinity of LBTs for Gd(3+) indicates their potential as the basis for engineering of peptide-based MRI agents. However, the lanthanide coordination state that enhances luminescence and affords tightest binding would not be ideal for applications of LBTs as contrast agents, due to the exclusion of water from the inner coordination sphere. Herein, we use structurally defined LBTs as the starting point for re-engineering the first coordination shell of the lanthanide ion to provide for high contrast through direct coordination of water to Gd(3+) (resulting in the single LBT peptide, m-sLBT). The effectiveness of LBTs as MRI contrast agents was examined in vitro through measurement of binding affinity and proton relaxivity. For imaging applications that require targeted observation, fusion to specific protein partners is desirable. However, a fusion protein comprising a concatenated double LBT (dLBT) as an N-terminal tag for the model protein ubiquitin had reduced relaxivity compared with the free dLBT peptide. This limitation was overcome by the use of a construct based on the m-sLBT sequence (q-dLBT-ubiquitin). The structural basis for the enhanced contrast was examined by comparison of the X-ray crystal structure of xq-dLBT-ubiquitin (wherein two tryptophan residues are replaced with serine), to that of dLBT-ubiquitin. The structure shows that the backbone conformational dynamics of the MRI variant may allow enhanced water exchange. This engineered LBT represents a first step in expanding the current base of specificity-targeted agents available.
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Tailoring encodable lanthanide-binding tags as MRI contrast agents.,Daughtry KD, Martin LJ, Sarraju A, Imperiali B, Allen KN Chembiochem. 2012 Nov 26;13(17):2567-74. doi: 10.1002/cbic.201200448. Epub 2012, Nov 13. PMID:23150430<ref>PMID:23150430</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 3vdz" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Synthetic construct sequences]]
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[[Category: Synthetic construct]]
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[[Category: Allen, K N]]
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[[Category: Allen KN]]
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[[Category: Daughtry, K D]]
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[[Category: Daughtry KD]]
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[[Category: Imperiali, B]]
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[[Category: Imperiali B]]
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[[Category: Martin, L J]]
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[[Category: Martin LJ]]
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[[Category: Surraju, A]]
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[[Category: Surraju A]]
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[[Category: De novo design]]
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[[Category: Gadolinium]]
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[[Category: Lanthanide binding tag]]
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[[Category: Metal binding protein]]
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[[Category: Mri contrast agent]]
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[[Category: Peptide-based contrast agent]]
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Current revision

Tailoring Encodable Lanthanide-Binding Tags as MRI Contrast Agents: xq-dSE3-Ubiquitin at 2.4 Angstroms

PDB ID 3vdz

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OCA

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