4bip: Difference between revisions
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New page: '''Unreleased structure''' The entry 4bip is ON HOLD Authors: Seitsonen, J.J.T., Shakeel, S., Susi, P., Pandurangan, A.P., Sinkovits, R.S., Hyvonen, H., Laurinmaki, P., Yla-Pelto, J., T... |
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==Homology model of coxsackievirus A7 (CAV7) full capsid proteins.== | |||
<SX load='4bip' size='340' side='right' viewer='molstar' caption='[[4bip]], [[Resolution|resolution]] 8.23Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4bip]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_A7 Coxsackievirus A7]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4agx 4agx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BIP 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]] 8.23Å</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=4bip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bip OCA], [https://pdbe.org/4bip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bip RCSB], [https://www.ebi.ac.uk/pdbsum/4bip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bip ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/I1T312_9ENTO I1T312_9ENTO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1A resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog - EV71 capsid - in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by approximately 5 degrees counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting. | |||
Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change.,Pandurangan AP, Shakeel S, Butcher SJ, Topf M J Struct Biol. 2014 Mar;185(3):427-39. doi: 10.1016/j.jsb.2013.12.003. Epub 2013 , Dec 12. PMID:24333899<ref>PMID:24333899</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4bip" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</SX> | |||
[[Category: Coxsackievirus A7]] | |||
[[Category: Large Structures]] | |||
[[Category: Butcher SJ]] | |||
[[Category: Hyvonen H]] | |||
[[Category: Hyypia T]] | |||
[[Category: Laurinmaki P]] | |||
[[Category: Pandurangan AP]] | |||
[[Category: Seitsonen JJT]] | |||
[[Category: Shakeel S]] | |||
[[Category: Sinkovits RS]] | |||
[[Category: Susi P]] | |||
[[Category: Topf M]] | |||
[[Category: Yla-Pelto J]] | |||
Latest revision as of 14:00, 9 May 2024
Homology model of coxsackievirus A7 (CAV7) full capsid proteins.Homology model of coxsackievirus A7 (CAV7) full capsid proteins.
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