<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-12960" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2025-09-08</depositionDate>
            <releaseDate>2025-11-30</releaseDate>
            <updateDate>2025-11-30</updateDate>
        </keyDates>
        <title>Cryo-EM micrographs of R2Tg retrotransposon initiating target-primed reverse transcription</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0003-4738-9503</authorORCID>
            <firstName>Max</firstName>
            <lastName>Wilkinson</lastName>
            <organization type="academic">Massachusetts Institute of Technology</organization>
            <street>75 Ames Street</street>
            <townOrCity>Cambridge</townOrCity>
            <stateOrProvince>Massachusetts</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>02142</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0003-0178-7995</authorORCID>
            <firstName>Feng</firstName>
            <lastName>Zhang</lastName>
            <organization type="academic">Broad Institute of Harvard and MIT</organization>
            <street>75 Ames Street</street>
            <townOrCity>Cambridge</townOrCity>
            <stateOrProvince>Massachusetts</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>02142</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0003-4738-9503">Wilkinson ME</author>
            <author authorORCID="0000-0003-0178-7995">Zhang F</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody></fundingBody>
                <code></code>
                <country></country>
            </grantReference>
        </grantSupport>
        <datasetSize units="TB">1.7</datasetSize>
        <entryDOI>10.6019/EMPIAR-12960</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>molecule</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-47091</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0002-7317-2669" order="1">Edmonds KK</author>
                    <author authorORCID="0000-0003-4738-9503" order="2">Wilkinson ME</author>
                    <author authorORCID="0000-0001-8732-6414" order="3">Strebinger D</author>
                    <author authorORCID="0000-0002-9496-8586" order="4">Chen H</author>
                    <author authorORCID="0000-0003-2445-7948" order="5">Lash B</author>
                    <author authorORCID="0009-0005-3701-913X" order="6">Schaefer CC</author>
                    <author authorORCID="0009-0001-2677-8262" order="7">Zhu S</author>
                    <author authorORCID="0000-0001-6598-8871" order="8">Liu D</author>
                    <author authorORCID="0000-0001-9223-5082" order="9">Zilberzwige-Tal S</author>
                    <author authorORCID="0000-0003-3945-7924" order="10">Ladha A</author>
                    <author authorORCID="0000-0001-5563-5829" order="11">Walsh ML</author>
                    <author order="12">Frangieh CJ</author>
                    <author order="13">Vaz Reay NA</author>
                    <author authorORCID="0000-0002-7850-9056" order="14">Macrae RK</author>
                    <author authorORCID="0000-0002-3090-9894" order="15">Wang X</author>
                    <author authorORCID="0000-0003-0178-7995" order="16">Zhang F</author>
                    <title>Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons</title>
                    <journal>Nature communications</journal>
                    <journalAbbreviation>Nat Commun</journalAbbreviation>
                    <country>United States</country>
                    <issue>1</issue>
                    <volume>16</volume>
                    <year>2025</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1038/s41467-025-61321-z</externalReferences>
                    <externalReferences type="pubmed">40603868</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Unaligned multi-frame movies of Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription</name>
        <directory>/data/Krios_20240308_TgD4</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>10628</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>5760</imageWidth>
            <pixelWidth>0.663</pixelWidth>
            <imageHeight>4092</imageHeight>
            <pixelHeight>0.663</pixelHeight>
        </dimensions>
        <details>RAW MICROGRAPHS AND REFINEMENT STAR FILE FOR R2Tg TPRT COMPLEX (EMD-47091; PDB 9DOU)
Data collected at MIT.nano on Thermo Scientific Titan Krios G3i cryo-TEM

Voltage		300 keV
Camera		Gatan K3, super-resolution mode with 2-fold binning by EPU
Energy filter	GIF, 20eV slit width
Magnification	130000
Pixel size	0.663 A/pix
Dose		59.6 e/A2
Exposure rate	25.7 e/pix/s
Exposure time	1.02 s
Fractions	40

Total mics	10628


GainReference.mrc was binned using 'rebin by two' in Digital Micrograph. It needs to be flipped for use in RELION motion correction (Gain flip: Flip upside down (1) ). It can probably be used as is for cryoSPARC.

particles.star contains metadata for the particle selected for the final reconstruction.</details>
        <segmentationList/>
        <micrographsFilePattern>data/Krios_20240308_TgD4/Images-Disc1/GridSquare_*/Data/FoilHole_*_fractions.tiff</micrographsFilePattern>
        <pickedParticlesFilePattern>data/particles.star</pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
