<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-13634" schemaVersion="0.65" public="true">
    <admin>
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        <keyDates>
            <depositionDate>2026-05-12</depositionDate>
            <releaseDate>2026-07-07</releaseDate>
            <updateDate>2026-07-07</updateDate>
        </keyDates>
        <title>Single particle cryo-EM dataset of yeast co-transcriptional pre-60S assembly intermediates Pwp1 RNP and Nop12 RNP</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-9373-4737</authorORCID>
            <firstName>Sebastian</firstName>
            <lastName>Klinge</lastName>
            <organization type="academic">Rockefeller University</organization>
            <street>1230 York Ave</street>
            <townOrCity>New York</townOrCity>
            <stateOrProvince>NY</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>10065</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-9373-4737</authorORCID>
            <firstName>Sebastian</firstName>
            <lastName>Klinge</lastName>
            <organization type="academic">Rockefeller University</organization>
            <street>1230 York Ave</street>
            <townOrCity>New York</townOrCity>
            <stateOrProvince>NY</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>10065</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0001-6463-916X">Piwowarczyk R</author>
            <author authorORCID="0000-0002-9373-4737">Klinge S</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</fundingBody>
                <code>5R01GM145950-03</code>
                <country>United States</country>
            </grantReference>
            <grantReference>
                <fundingBody>Chan Zuckerberg Initiative</fundingBody>
                <code>2023-332391</code>
                <country>United States</country>
            </grantReference>
        </grantSupport>
        <datasetSize units="TB">32.7</datasetSize>
        <entryDOI>10.6019/EMPIAR-13634</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>molecule</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-75577</emdbEntry>
            <emdbEntry>EMD-75578</emdbEntry>
            <emdbEntry>EMD-75579</emdbEntry>
            <emdbEntry>EMD-75580</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="true">
                    <author authorORCID="0000-0001-6463-916X" order="1">Piwowarczyk R</author>
                    <author authorORCID="0000-0002-9373-4737" order="2">Klinge S</author>
                    <title>Mechanism for the initiation of co-transcriptional pre-60  &lt;i&gt;S&lt;/i&gt;  assembly</title>
                    <journal>bioRxiv</journal>
                    <journalAbbreviation></journalAbbreviation>
                    <country></country>
                    <year>2026</year>
                    <externalReferences type="doi">10.64898/2026.05.22.727207</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Unaligned multi-frame micrograph movies of the co-transcriptional pre-60S intermediates -- Dataset 3</name>
        <directory>/data/ds3</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>30768</numImagesOrTiltSeries>
        <framesPerImage>50</framesPerImage>
        <frameRange>
            <frameRangeMin>1</frameRangeMin>
            <frameRangeMax>50</frameRangeMax>
        </frameRange>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.54</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.54</pixelHeight>
        </dimensions>
        <details>The dataset was collected on a Titan Krios electron microscope operating at 300 kV equipped with an energy filter (slit width 20 eV), a Cs corrector and a K3 Summit detector set in super-resolution mode. Unaligned multi-frame micrographs were recorded at a nominal magnification of 64,000× with a pixel size of 0.54 Å/pixel, a defocus range of -0.7 to -1.7 µm, and a total dose of 50.0 e-/Å2 (50 frames). The gain reference was applied on-the-fly during data collection.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Unaligned multi-frame micrograph movies of the co-transcriptional pre-60S intermediates -- Dataset 4</name>
        <directory>/data/ds4</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>9708</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <frameRange>
            <frameRangeMin>1</frameRangeMin>
            <frameRangeMax>40</frameRangeMax>
        </frameRange>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.545</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.545</pixelHeight>
        </dimensions>
        <details>The dataset was collected on a Titan Krios electron microscope operating at 300 kV equipped with an energy filter (slit width 20 eV), a K3 Summit detector set in super-resolution mode. Unaligned multi-frame micrographs were recorded at a nominal magnification of 81,000× with a pixel size of 0.545 Å/pixel, a defocus range of -0.6 to -1.7 µm, and a total dose of 50.0 e-/Å2 (40 frames). The gain reference was applied on-the-fly during data collection.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Unaligned multi-frame micrograph movies of the co-transcriptional pre-60S intermediates -- Dataset 5</name>
        <directory>/data/ds5</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>10799</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <frameRange>
            <frameRangeMin>1</frameRangeMin>
            <frameRangeMax>40</frameRangeMax>
        </frameRange>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.545</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.545</pixelHeight>
        </dimensions>
        <details>The dataset was collected on a Titan Krios electron microscope operating at 300 kV equipped with an energy filter (slit width 20 eV), a K3 Summit detector set in super-resolution mode. Unaligned multi-frame micrographs were recorded at a nominal magnification of 81,000× with a pixel size of 0.545 Å/pixel, a defocus range of -0.6 to -1.7 µm, and a total dose of 50.0 e-/Å2 (40 frames). The gain reference was applied on-the-fly during data collection.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Unaligned multi-frame micrograph movies of the co-transcriptional pre-60S intermediates -- Dataset 6</name>
        <directory>/data/ds6</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>10632</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <frameRange>
            <frameRangeMin>1</frameRangeMin>
            <frameRangeMax>40</frameRangeMax>
        </frameRange>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.545</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.545</pixelHeight>
        </dimensions>
        <details>The dataset was collected on a Titan Krios electron microscope operating at 300 kV equipped with an energy filter (slit width 20 eV), a K3 Summit detector set in super-resolution mode. Unaligned multi-frame micrographs were recorded at a nominal magnification of 81,000× with a pixel size of 0.545 Å/pixel, a defocus range of -0.6 to -1.7 µm, and a total dose of 50.0 e-/Å2 (40 frames). The gain reference was applied on-the-fly during data collection.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Polished particle stacks of Pwp1-RNP and Nop12-RNP co-transcriptional pre-60S intermediates</name>
        <directory>/data/particles</directory>
        <category>picked particles - multiframe - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
        <numImagesOrTiltSeries>2544054</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>SIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>300</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>300</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>Particle sets used to reconstruct the pre-60S intermediates from all datasets. The particles were polished in cryoSPARC. For each reconstruction, the provided STAR file contains the patch-CTF estimated defocus and CTF corrections, as well as the final Euler angles, shifts, and micrograph coordinates.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
