<entry xmlns="http://pdbe.org/empiar" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://ftp.ebi.ac.uk/pub/databases/emtest/empiar/schema/empiar.xsd" accessionCode="EMPIAR-10387" schemaVersion="0.65" public="true">
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        <keyDates>
            <depositionDate>2020-03-26</depositionDate>
            <releaseDate>2020-06-30</releaseDate>
            <updateDate>2020-06-30</updateDate>
        </keyDates>
        <title>Structural basis for strand-transfer inhibitor binding to HIV intasomes</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0003-1333-9102</authorORCID>
            <firstName>Dario</firstName>
            <lastName>Oliveira Passos</lastName>
            <organization type="academic">Salk Institute</organization>
            <street>10010 N Torrey Pines</street>
            <townOrCity>San Diego</townOrCity>
            <stateOrProvince>California</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>92037</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-8124-7472</authorORCID>
            <firstName>Dmitry</firstName>
            <lastName>Lyumkis</lastName>
            <organization type="academic">Salk Institute</organization>
            <street>10010 N Torrey Pines</street>
            <townOrCity>San Diego</townOrCity>
            <stateOrProvince>California</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>92037</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0003-1333-9102">Passos DO</author>
            <author>Li M</author>
            <author authorORCID="0000-0002-7150-5802">Jóźwik IK</author>
            <author authorORCID="0000-0003-1006-6364">Zhao XZ</author>
            <author authorORCID="0000-0003-4622-3747">Santos-Martins D</author>
            <author authorORCID="0000-0001-9640-4189">Yang R</author>
            <author>Smith SJ</author>
            <author authorORCID="0000-0001-7563-4743">Jeon Y</author>
            <author authorORCID="0000-0002-5964-7111">Forli S</author>
            <author>Hughes SH</author>
            <author authorORCID="0000-0001-9925-8586">Burke TR</author>
            <author authorORCID="0000-0001-9516-6385">Craigie R</author>
            <author authorORCID="0000-0002-8124-7472">Lyumkis D</author>
        </authorsList>
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        <entryDOI>10.6019/EMPIAR-10387</entryDOI>
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    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-20484</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0003-1333-9102" order="1">Passos DO</author>
                    <author order="2">Li M</author>
                    <author authorORCID="0000-0002-7150-5802" order="3">Jóźwik IK</author>
                    <author authorORCID="0000-0003-1006-6364" order="4">Zhao XZ</author>
                    <author authorORCID="0000-0003-4622-3747" order="5">Santos-Martins D</author>
                    <author authorORCID="0000-0001-9640-4189" order="6">Yang R</author>
                    <author order="7">Smith SJ</author>
                    <author authorORCID="0000-0001-7563-4743" order="8">Jeon Y</author>
                    <author authorORCID="0000-0002-5964-7111" order="9">Forli S</author>
                    <author order="10">Hughes SH</author>
                    <author authorORCID="0000-0001-9925-8586" order="11">Burke TR</author>
                    <author authorORCID="0000-0001-9516-6385" order="12">Craigie R</author>
                    <author authorORCID="0000-0002-8124-7472" order="13">Lyumkis D</author>
                    <title>Structural basis for strand-transfer inhibitor binding to HIV intasomes</title>
                    <journal>Science (New York, N.Y.)</journal>
                    <journalAbbreviation>Science</journalAbbreviation>
                    <country>United States</country>
                    <issue>6479</issue>
                    <volume>367</volume>
                    <firstPage>810</firstPage>
                    <lastPage>814</lastPage>
                    <year>2020</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1126/science.aay8015</externalReferences>
                    <externalReferences type="pubmed">32001521</externalReferences>
                    <details>Compressed movies of HIV intasomes bound to the compound 4d. Movies contain 80 raw frames each, accumulating 45 electron per square Angstrom in an 8 second exposure. Pixel size is 0.79.</details>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Aligned, summed and exposure weighted micrographs of HIV-1 intasome bound to compound 4d.</name>
        <directory>/data/Sums</directory>
        <category>micrographs - single frame</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>2022</numImagesOrTiltSeries>
        <framesPerImage>77</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>3710</imageWidth>
            <pixelWidth>0.79</pixelWidth>
            <imageHeight>3838</imageHeight>
            <pixelHeight>0.79</pixelHeight>
        </dimensions>
        <details>Aligned, summed and exposure weighted micrographs of HIV-1 intasome bound to compound 4d. Micrographs were aligned and summed using MotionCor2, with 5 by 5 patch and exposure weighting. The first 3 frames, which had the most beam-induced movement, were discarded.

Regarding particle stack of HIV-1 intasome bound to compound 4d. Particles were extracted from aligned, exposured weighted and summed micrographs. This stack contains 138,770 particles (384 x 384 pixels) and was processed in cisTEM. Both *mrc and *par files are included.</details>
        <segmentationList/>
        <micrographsFilePattern>data/Sums/*DW.mrc</micrographsFilePattern>
        <pickedParticlesFilePattern>data/Particle-Stack/18jul30a_4d_F3-77_vol180-1_2-88A.mrc</pickedParticlesFilePattern>
        <pickedParticlesDirectory>data/Particle-Stack</pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Unaligned raw movies of HIV-1 intasome bound to compound 4d</name>
        <directory>/data/Rawdata</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>2024</numImagesOrTiltSeries>
        <framesPerImage>80</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>3710</imageWidth>
            <pixelWidth>0.79</pixelWidth>
            <imageHeight>3838</imageHeight>
            <pixelHeight>0.79</pixelHeight>
        </dimensions>
        <details>Unaligned raw multi-frame movies of HIV-1 intasome bound to compound 4d. Movies were collected with a stage tilt angle set to 20, 30, or 40 degrees. The gain normalization reference image (norm) is included for each of the 3 sessions.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
