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            <depositionDate>2025-09-12</depositionDate>
            <releaseDate>2026-03-16</releaseDate>
            <updateDate>2026-03-16</updateDate>
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        <title>Medium-resolution cryo-EM structure of the Danio rerio tRNA ligase complex</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0001-5582-2851</authorORCID>
            <firstName>Mariusz</firstName>
            <lastName>Czarnocki-Cieciura</lastName>
            <organization type="academic">International Institute of Molecular and Cell Biology in Warsaw</organization>
            <street>4 Ks. Trojdena Street</street>
            <townOrCity>Warsaw</townOrCity>
            <country>Poland</country>
            <postOrZipCode>02-106</postOrZipCode>
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            <firstName>Marcin</firstName>
            <lastName>Nowotny</lastName>
            <organization type="academic">International Institute of Molecular and Cell Biology in Warsaw</organization>
            <street>4 Ks. Trojdena Street</street>
            <townOrCity>Warsaw</townOrCity>
            <country>Poland</country>
            <postOrZipCode>02-109</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0002-2328-9703">Chamera S</author>
            <author authorORCID="0000-0001-9915-0305">Zajko W</author>
            <author authorORCID="0000-0001-5582-2851">Czarnocki-Cieciura M</author>
            <author authorORCID="0000-0003-1251-1492">Jaciuk M</author>
            <author authorORCID="0000-0003-3885-3845">Koziej Ł</author>
            <author authorORCID="0000-0001-6536-2940">Nowak J</author>
            <author authorORCID="0000-0002-0999-0560">Wycisk K</author>
            <author authorORCID="0000-0002-3865-1218">Sroka M</author>
            <author authorORCID="0000-0002-3544-7211">Chramiec-Głąbik A</author>
            <author authorORCID="0000-0002-9482-6588">Śmietański M</author>
            <author authorORCID="0000-0002-8011-2162">Gołębiowski F</author>
            <author authorORCID="0000-0002-1071-3405">Warmiński M</author>
            <author authorORCID="0000-0001-7633-788X">Jemielity J</author>
            <author authorORCID="0000-0003-2815-7133">Glatt S</author>
            <author authorORCID="0000-0001-8632-0977">Nowotny M</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody>Polish National Science Centre</fundingBody>
                <code>2019/33/B/NZ1/02839</code>
                <country>Poland</country>
            </grantReference>
            <grantReference>
                <fundingBody>Other government</fundingBody>
                <code>1/SOL/2021/2</code>
                <country>Poland</country>
            </grantReference>
            <grantReference>
                <fundingBody>European Research Council (ERC)</fundingBody>
                <code>101001394</code>
                <country>Poland</country>
            </grantReference>
        </grantSupport>
        <datasetSize units="TB">3.9</datasetSize>
        <entryDOI>10.6019/EMPIAR-13357</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>molecule</scale>
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    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-50108</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0002-2328-9703" order="1">Chamera S</author>
                    <author authorORCID="0000-0001-9915-0305" order="2">Zajko W</author>
                    <author authorORCID="0000-0001-5582-2851" order="3">Czarnocki-Cieciura M</author>
                    <author authorORCID="0000-0003-1251-1492" order="4">Jaciuk M</author>
                    <author authorORCID="0000-0003-3885-3845" order="5">Koziej Ł</author>
                    <author authorORCID="0000-0001-6536-2940" order="6">Nowak J</author>
                    <author authorORCID="0000-0002-0999-0560" order="7">Wycisk K</author>
                    <author authorORCID="0000-0002-3865-1218" order="8">Sroka M</author>
                    <author authorORCID="0000-0002-3544-7211" order="9">Chramiec-Głąbik A</author>
                    <author authorORCID="0000-0002-9482-6588" order="10">Śmietański M</author>
                    <author authorORCID="0000-0002-8011-2162" order="11">Gołębiowski F</author>
                    <author authorORCID="0000-0002-1071-3405" order="12">Warmiński M</author>
                    <author authorORCID="0000-0001-7633-788X" order="13">Jemielity J</author>
                    <author authorORCID="0000-0003-2815-7133" order="14">Glatt S</author>
                    <author authorORCID="0000-0001-8632-0977" order="15">Nowotny M</author>
                    <title>Structural and biochemical characterization of the 3'-5' tRNA splicing ligases</title>
                    <journal>The Journal of biological chemistry</journal>
                    <journalAbbreviation>J Biol Chem</journalAbbreviation>
                    <country></country>
                    <issue>5</issue>
                    <volume>301</volume>
                    <year>2025</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1016/j.jbc.2025.108506</externalReferences>
                    <externalReferences type="pubmed">40220997</externalReferences>
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        <name>Unaligned multi-frame movies of Danio rerio tRNA ligase complex (full-length version)</name>
        <directory>/data/Movies</directory>
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        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>10703</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>5760</imageWidth>
            <pixelWidth>0.86</pixelWidth>
            <imageHeight>4092</imageHeight>
            <pixelHeight>0.86</pixelHeight>
        </dimensions>
        <details>Gain-corrected, unaligned multi-frame movies collected with Krios G3i microscope + K3 detector (superresolution mode, binned 2x with EPU). Voltage: 300 kV; spherical aberration: 2.7; dose per frame: 1 e/A^2 (total dose: 39.41 e/A^2 fractionated over 40 frames). Defocus range (nominal): -2.1, -1.8, -1.5, -1.2, -0.9 µm. Objective aperture retracted, C2 aperture: 50 µm.</details>
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        <pickedParticlesDirectory>data/particles</pickedParticlesDirectory>
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    <imageSet>
        <name>Aligned particles of Danio rerio tRNA ligase complex (full-length version)</name>
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        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
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        <framesPerImage>1</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
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            <imageHeight>320</imageHeight>
            <pixelHeight>0.86</pixelHeight>
        </dimensions>
        <details>Aligned particles with corresponding Relion-3 STAR file. Micrographs were initially binned 2x during Motion correction.</details>
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