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6cvm

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Current revision (14:30, 13 March 2024) (edit) (undo)
 
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<SX load='6cvm' size='340' side='right' viewer='molstar' caption='[[6cvm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<SX load='6cvm' size='340' side='right' viewer='molstar' caption='[[6cvm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6cvm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6CVM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6cvm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CVM 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTQ:2-PHENYLETHYL+1-THIO-BETA-D-GALACTOPYRANOSIDE'>PTQ</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">Electron Microscopy, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTQ:2-PHENYLETHYL+1-THIO-BETA-D-GALACTOPYRANOSIDE'>PTQ</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6cvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvm OCA], [http://pdbe.org/6cvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cvm RCSB], [http://www.ebi.ac.uk/pdbsum/6cvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvm ProSAT]</span></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=6cvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvm OCA], [https://pdbe.org/6cvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cvm RCSB], [https://www.ebi.ac.uk/pdbsum/6cvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvm 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/BGAL_ECOLI BGAL_ECOLI]
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The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for beta-galactosidase bound to the inhibitor phenylethyl beta-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at approximately 1.5 A resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.
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Atomic Resolution Cryo-EM Structure of beta-Galactosidase.,Bartesaghi A, Aguerrebere C, Falconieri V, Banerjee S, Earl LA, Zhu X, Grigorieff N, Milne JLS, Sapiro G, Wu X, Subramaniam S Structure. 2018 May 10. pii: S0969-2126(18)30129-1. doi:, 10.1016/j.str.2018.04.004. PMID:29754826<ref>PMID:29754826</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 6cvm" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Galactosidase 3D structures|Galactosidase 3D structures]]
*[[Galactosidase 3D structures|Galactosidase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</SX>
</SX>
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[[Category: Beta-galactosidase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ecoli]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Banerjee, S]]
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[[Category: Banerjee S]]
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[[Category: Bartesaghi, A]]
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[[Category: Bartesaghi A]]
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[[Category: Milne, J L.S]]
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[[Category: Milne JLS]]
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[[Category: Subramaniam, S]]
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[[Category: Subramaniam S]]
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[[Category: Zhu, X]]
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[[Category: Zhu X]]
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[[Category: Computer-aided drug discovery]]
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[[Category: Drift correction]]
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[[Category: Drug discovery]]
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[[Category: Hydrolase]]
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[[Category: Precision medicine]]
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[[Category: Radiation damage]]
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Current revision

Atomic resolution cryo-EM structure of beta-galactosidase

6cvm, resolution 1.90Å

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