<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-13642" schemaVersion="0.65" public="true">
    <admin>
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        <keyDates>
            <depositionDate>2024-03-01</depositionDate>
            <releaseDate>2026-06-25</releaseDate>
            <updateDate>2026-06-25</updateDate>
        </keyDates>
        <title>Cryo-EM single particle micrographs of hypomethylated 80S ribosomes</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0003-2046-9861</authorORCID>
            <firstName>Hong</firstName>
            <lastName>Li</lastName>
            <organization type="academic">Department of Structural Biology, Van Andel Institute</organization>
            <townOrCity>Grand Rapids</townOrCity>
            <stateOrProvince>Michigan</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>49503</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0003-2046-9861</authorORCID>
            <firstName>Hong</firstName>
            <lastName>Li</lastName>
            <organization type="academic">Department of Structural Biology, Van Andel Institute</organization>
            <townOrCity>Grand Rapids</townOrCity>
            <stateOrProvince>Michigan</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>49503</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0003-0485-2780">Zhao Y</author>
            <author authorORCID="0000-0003-2046-9861">Li H</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody></fundingBody>
                <code></code>
                <country></country>
            </grantReference>
        </grantSupport>
        <datasetSize units="TB">24.2</datasetSize>
        <entryDOI>10.6019/EMPIAR-13642</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>molecule</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-40990</emdbEntry>
            <emdbEntry>EMD-40991</emdbEntry>
            <emdbEntry>EMD-40992</emdbEntry>
            <emdbEntry>EMD-40993</emdbEntry>
            <emdbEntry>EMD-71745</emdbEntry>
            <emdbEntry>EMD-40997</emdbEntry>
            <emdbEntry>EMD-40998</emdbEntry>
            <emdbEntry>EMD-40999</emdbEntry>
            <emdbEntry>EMD-41000</emdbEntry>
            <emdbEntry>EMD-41001</emdbEntry>
            <emdbEntry>EMD-41002</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author order="1">Zhao Y</author>
                    <author order="2">Rai J</author>
                    <author order="3">Cohen LN</author>
                    <author order="4">Shu Y</author>
                    <author order="5">Xu C</author>
                    <author order="6">Goswami H</author>
                    <author order="7">Chen X</author>
                    <author order="8">Jin H</author>
                    <author order="9">Marchand V</author>
                    <author order="10">Motorin Y</author>
                    <author order="11">Ghalei H</author>
                    <author order="12">Li H</author>
                    <title>2'-O-Methylation maintains ribosome structural and translation integrity</title>
                    <journal>Molecular cell</journal>
                    <journalAbbreviation>Mol Cell</journalAbbreviation>
                    <country></country>
                    <issue>8</issue>
                    <volume>86</volume>
                    <firstPage>1495</firstPage>
                    <lastPage>1510.e7</lastPage>
                    <year>2026</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1016/j.molcel.2026.03.008</externalReferences>
                    <externalReferences type="pubmed">41928510</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>unaligned multi-frame micrographs of yeast hypomethylated 80S ribosome treated with hygromycin B</name>
        <directory>/data/HygromycinB-treated</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>EER</headerFormat>
        <dataFormat>EER</dataFormat>
        <numImagesOrTiltSeries>9063</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>BIT</voxelType>
        <dimensions>
            <imageWidth>4096</imageWidth>
            <pixelWidth>0.365</pixelWidth>
            <imageHeight>4096</imageHeight>
            <pixelHeight>0.365</pixelHeight>
        </dimensions>
        <details>This dataset was collected on Falcon 4 camera in EER mode using Leginon, with a super-resolution pixel size of 0.365 and a  total dose of 55.20 e–/Å2. The authors used EER fractionation of 32 and dose per frame of 0.82 with a binning factor 2 for motion correction.</details>
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        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>unaligned multi-frame micrographs of yeast nutrient limiting hypomethylated 80S ribosome</name>
        <directory>/data/Nutrient-limiting</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>10148</numImagesOrTiltSeries>
        <framesPerImage>60</framesPerImage>
        <voxelType>BIT</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.53</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.53</pixelHeight>
        </dimensions>
        <details>This dataset was collected on K3 camera at 81k magnification using EPU, with a super-resolution pixel size of 0.53 and a  total dose of 60 e–/Å2 spreading over 60 frames. Gain file is also provided. Gain orientation in Relion: no rotation, Flip upside-down;  in cryosparc: no rotation, no flip.</details>
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        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>unaligned multi-frame micrographs of yeast hypomethylated polysomes at 81K magnification</name>
        <directory>/data/Polysome-81K</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>7659</numImagesOrTiltSeries>
        <framesPerImage>60</framesPerImage>
        <voxelType>BIT</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.53</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.53</pixelHeight>
        </dimensions>
        <details>This dataset was collected on K3 camera at 81k magnification using EPU, with a super-resolution pixel size of 0.53 and a  total dose of 60 e–/Å2 spreading over 60 frames. Gain file is also provided. Gain orientation in Relion: no rotation, Flip upside-down;  in cryosparc: no rotation, no flip.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>unaligned multi-frame micrographs of yeast hypomethylated polysomes at 105K magnification</name>
        <directory>/data/Polysome-105K</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>5585</numImagesOrTiltSeries>
        <framesPerImage>60</framesPerImage>
        <voxelType>BIT</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.415</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.415</pixelHeight>
        </dimensions>
        <details>This dataset was collected on K3 camera at 81k magnification using EPU, with a super-resolution pixel size of 0.415 and a  total dose of 60 e–/Å2 spreading over 60 frames. Gain file is also provided. Gain orientation in Relion: no rotation, Flip upside-down;  in cryosparc: no rotation, no flip.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>unaligned multi-frame micrographs of yeast hypomethylated 80S ribosome bound with TSV-IRES, eEF2, sodarin</name>
        <directory>/data/TSV-bound</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>7369</numImagesOrTiltSeries>
        <framesPerImage>60</framesPerImage>
        <voxelType>BIT</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.53</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.53</pixelHeight>
        </dimensions>
        <details>This dataset was collected on K3 camera at 81k magnification using serialEM, with a super-resolution pixel size of 0.53 and a  total dose of 60 e–/Å2 spreading over 60 frames. Gain file is also provided.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
