8b7v: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-'''Unreleased structure'''
-The entry 8b7v is ON HOLD
+==Automated simulation-based refinement of maltoporin into a cryo-EM density==
+<StructureSection load='8b7v' size='340' side='right'caption='[[8b7v]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8b7v]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8B7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B7V FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3&#8491;</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=8b7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b7v OCA], [https://pdbe.org/8b7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b7v RCSB], [https://www.ebi.ac.uk/pdbsum/8b7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b7v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A2X5NX10_ECOLX A0A2X5NX10_ECOLX] Involved in the transport of maltose and maltodextrins.[HAMAP-Rule:MF_01301]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins-a category that constitutes a disproportionate share of drug targets. We present a protocol for using density-guided molecular dynamics simulations to automatically refine atomistic models into membrane protein cryo-EM maps. Using adaptive force density-guided simulations as implemented in the GROMACS molecular dynamics package, we show how automated model refinement of a membrane protein is achieved without the need to manually tune the fitting force ad hoc. We also present selection criteria to choose the best-fit model that balances stereochemistry and goodness of fit. The proposed protocol was used to refine models into a new cryo-EM density of the membrane protein maltoporin, either in a lipid bilayer or detergent micelle, and we found that results do not substantially differ from fitting in solution. Fitted structures satisfied classical model-quality metrics and improved the quality and the model-to-map correlation of the x-ray starting structure. Additionally, the density-guided fitting in combination with generalized orientation-dependent all-atom potential was used to correct the pixel-size estimation of the experimental cryo-EM density map. This work demonstrates the applicability of a straightforward automated approach to fitting membrane protein cryo-EM densities. Such computational approaches promise to facilitate rapid refinement of proteins under different conditions or with various ligands present, including targets in the highly relevant superfamily of membrane proteins.
-Authors:
+Automated simulation-based membrane protein refinement into cryo-EM data.,Yvonnesdotter L, Rovsnik U, Blau C, Lycksell M, Howard RJ, Lindahl E Biophys J. 2023 Jun 5:S0006-3495(23)00367-3. doi: 10.1016/j.bpj.2023.05.033. PMID:37277992<ref>PMID:37277992</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8b7v" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Blau C]]
+[[Category: Howard RJ]]
+[[Category: Lindahl E]]
+[[Category: Lycksell M]]
+[[Category: Rovsnik U]]
+[[Category: Yvonnesdotter L]]