Enhancement of tomogram interpretability using the locked self-rotation function
[Display omitted] •Self-rotation function can be used to find orientations of particles in tomograms.•Once the orientations have been determined the symmetry-averaged maps can be produced.•The symmetry-averaged maps may be helpful to reject particles that are outliers.•Finally, the inter-particle av...
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Veröffentlicht in: | Journal of structural biology 2019-03, Vol.205 (3), p.53-58 |
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container_title | Journal of structural biology |
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creator | Fokine, Andrei Khare, Baldeep Sun, Yingyuan Rossmann, Michael G. |
description | [Display omitted]
•Self-rotation function can be used to find orientations of particles in tomograms.•Once the orientations have been determined the symmetry-averaged maps can be produced.•The symmetry-averaged maps may be helpful to reject particles that are outliers.•Finally, the inter-particle averaged map can be calculated to improve interpretability.
The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability. Sub-tomograms of the icosahedral bacteriophage phiX174 are used to demonstrate the procedure. |
doi_str_mv | 10.1016/j.jsb.2019.01.006 |
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•Self-rotation function can be used to find orientations of particles in tomograms.•Once the orientations have been determined the symmetry-averaged maps can be produced.•The symmetry-averaged maps may be helpful to reject particles that are outliers.•Finally, the inter-particle averaged map can be calculated to improve interpretability.
The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability. Sub-tomograms of the icosahedral bacteriophage phiX174 are used to demonstrate the procedure.</description><identifier>ISSN: 1047-8477</identifier><identifier>EISSN: 1095-8657</identifier><identifier>DOI: 10.1016/j.jsb.2019.01.006</identifier><identifier>PMID: 30742896</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Bacteriophage phi X 174 - ultrastructure ; Capsid - ultrastructure ; Cryo-electron tomography ; Cryoelectron Microscopy - methods ; Electron Microscope Tomography - methods ; Image Processing, Computer-Assisted - statistics & numerical data ; Locked self-rotation function ; Macromolecular complexes ; Point group symmetry ; Rotation ; Virus structure</subject><ispartof>Journal of structural biology, 2019-03, Vol.205 (3), p.53-58</ispartof><rights>2019 Elsevier Inc.</rights><rights>Copyright © 2019 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c403t-89ec48aa5c5b35a675ac54f064035a17a4b13dcb24c472de5c03dbf35bf22ae93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jsb.2019.01.006$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30742896$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fokine, Andrei</creatorcontrib><creatorcontrib>Khare, Baldeep</creatorcontrib><creatorcontrib>Sun, Yingyuan</creatorcontrib><creatorcontrib>Rossmann, Michael G.</creatorcontrib><title>Enhancement of tomogram interpretability using the locked self-rotation function</title><title>Journal of structural biology</title><addtitle>J Struct Biol</addtitle><description>[Display omitted]
•Self-rotation function can be used to find orientations of particles in tomograms.•Once the orientations have been determined the symmetry-averaged maps can be produced.•The symmetry-averaged maps may be helpful to reject particles that are outliers.•Finally, the inter-particle averaged map can be calculated to improve interpretability.
The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability. Sub-tomograms of the icosahedral bacteriophage phiX174 are used to demonstrate the procedure.</description><subject>Bacteriophage phi X 174 - ultrastructure</subject><subject>Capsid - ultrastructure</subject><subject>Cryo-electron tomography</subject><subject>Cryoelectron Microscopy - methods</subject><subject>Electron Microscope Tomography - methods</subject><subject>Image Processing, Computer-Assisted - statistics & numerical data</subject><subject>Locked self-rotation function</subject><subject>Macromolecular complexes</subject><subject>Point group symmetry</subject><subject>Rotation</subject><subject>Virus structure</subject><issn>1047-8477</issn><issn>1095-8657</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU9r3DAQxUVpaP60H6CX4GMvdkayJNsECiWkTSCQHJKzkOXxrra2tJHkQL59tGwS2ktOMzBv3jzmR8h3ChUFKs821Sb2FQPaVUArAPmJHFHoRNlK0Xze9bwpW940h-Q4xg0AcMroF3JYQ8NZ28kjcnfp1toZnNGlwo9F8rNfBT0X1iUM24BJ93ay6blYonWrIq2xmLz5i0MRcRrL4JNO1rtiXJzZNV_JwainiN9e6wl5-H15f3FV3tz-ub74dVMaDnUq2w4Nb7UWRvS10LIR2gg-gsxToWmjeU_rwfSMG96wAYWBeujHWvQjYxq7-oT83Ptul37GweT8QU9qG-ysw7Py2qr_J86u1co_KckZtFJmgx-vBsE_LhiTmm00OE3aoV-iYrQVQuQ8NEvpXmqCjzHg-H6GgtqRUBuVSagdCQVUZRJ55_TffO8bb6_PgvO9APOXniwGFY3FjGKwAU1Sg7cf2L8ASwOcLQ</recordid><startdate>20190301</startdate><enddate>20190301</enddate><creator>Fokine, Andrei</creator><creator>Khare, Baldeep</creator><creator>Sun, Yingyuan</creator><creator>Rossmann, Michael G.</creator><general>Elsevier Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20190301</creationdate><title>Enhancement of tomogram interpretability using the locked self-rotation function</title><author>Fokine, Andrei ; Khare, Baldeep ; Sun, Yingyuan ; Rossmann, Michael G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c403t-89ec48aa5c5b35a675ac54f064035a17a4b13dcb24c472de5c03dbf35bf22ae93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Bacteriophage phi X 174 - ultrastructure</topic><topic>Capsid - ultrastructure</topic><topic>Cryo-electron tomography</topic><topic>Cryoelectron Microscopy - methods</topic><topic>Electron Microscope Tomography - methods</topic><topic>Image Processing, Computer-Assisted - statistics & numerical data</topic><topic>Locked self-rotation function</topic><topic>Macromolecular complexes</topic><topic>Point group symmetry</topic><topic>Rotation</topic><topic>Virus structure</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fokine, Andrei</creatorcontrib><creatorcontrib>Khare, Baldeep</creatorcontrib><creatorcontrib>Sun, Yingyuan</creatorcontrib><creatorcontrib>Rossmann, Michael G.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of structural biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fokine, Andrei</au><au>Khare, Baldeep</au><au>Sun, Yingyuan</au><au>Rossmann, Michael G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Enhancement of tomogram interpretability using the locked self-rotation function</atitle><jtitle>Journal of structural biology</jtitle><addtitle>J Struct Biol</addtitle><date>2019-03-01</date><risdate>2019</risdate><volume>205</volume><issue>3</issue><spage>53</spage><epage>58</epage><pages>53-58</pages><issn>1047-8477</issn><eissn>1095-8657</eissn><abstract>[Display omitted]
•Self-rotation function can be used to find orientations of particles in tomograms.•Once the orientations have been determined the symmetry-averaged maps can be produced.•The symmetry-averaged maps may be helpful to reject particles that are outliers.•Finally, the inter-particle averaged map can be calculated to improve interpretability.
The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability. Sub-tomograms of the icosahedral bacteriophage phiX174 are used to demonstrate the procedure.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>30742896</pmid><doi>10.1016/j.jsb.2019.01.006</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Bacteriophage phi X 174 - ultrastructure Capsid - ultrastructure Cryo-electron tomography Cryoelectron Microscopy - methods Electron Microscope Tomography - methods Image Processing, Computer-Assisted - statistics & numerical data Locked self-rotation function Macromolecular complexes Point group symmetry Rotation Virus structure |
title | Enhancement of tomogram interpretability using the locked self-rotation function |
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