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        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2026-06-11</depositionDate>
            <releaseDate>2026-06-28</releaseDate>
            <updateDate>2026-06-28</updateDate>
        </keyDates>
        <title>Cryo-EM Structures of Methylation-dependent Cas9</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="0009-0000-8986-0725">Shu Y</author>
            <author authorORCID="0000-0003-0485-2780">Zhao Y</author>
            <author authorORCID="0000-0003-2046-9861">Li H</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody>National Institutes of Health (NIH)</fundingBody>
                <code>S10RR025080</code>
                <country>United States</country>
            </grantReference>
            <grantReference>
                <fundingBody>National Institutes of Health (NIH)</fundingBody>
                <code>U24GM116788</code>
                <country>United States</country>
            </grantReference>
            <grantReference>
                <fundingBody>National Institutes of Health (NIH)</fundingBody>
                <code>S10RR024564</code>
                <country>United States</country>
            </grantReference>
            <grantReference>
                <fundingBody>Department of Energy (DOE, United States)</fundingBody>
                <code>KP160711</code>
                <country>United States</country>
            </grantReference>
        </grantSupport>
        <datasetSize units="TB">11.1</datasetSize>
        <entryDOI>10.6019/EMPIAR-13658</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>molecule</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-44859</emdbEntry>
            <emdbEntry>EMD-43769</emdbEntry>
            <emdbEntry>EMD-43771</emdbEntry>
            <emdbEntry>EMD-43772</emdbEntry>
            <emdbEntry>EMD-43770</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author order="1">Roth MO</author>
                    <author authorORCID="0009-0000-8986-0725" order="2">Shu Y</author>
                    <author authorORCID="0000-0003-0485-2780" order="3">Zhao Y</author>
                    <author order="4">Trasanidou D</author>
                    <author order="5">Hoffman RD</author>
                    <author order="6">Südfeld C</author>
                    <author order="7">Bouzetos E</author>
                    <author order="8">Trasanidis N</author>
                    <author order="9">Zawrotny M</author>
                    <author order="10">Gelasco MK</author>
                    <author order="11">Medina ML</author>
                    <author order="12">Das A</author>
                    <author order="13">Rai J</author>
                    <author order="14">Goswami HN</author>
                    <author order="15">Wang B</author>
                    <author order="16">van der Oost J</author>
                    <author authorORCID="0000-0003-2046-9861" order="17">Li H</author>
                    <title>Molecular basis for methylation-sensitive editing by Cas9</title>
                    <journal>Nature</journal>
                    <journalAbbreviation>Nature</journalAbbreviation>
                    <country></country>
                    <issue>8116</issue>
                    <volume>653</volume>
                    <firstPage>1229</firstPage>
                    <lastPage>1239</lastPage>
                    <year>2026</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1038/s41586-026-10384-z</externalReferences>
                    <externalReferences type="pubmed">41986708</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>unaligned multi-frame micrographs of ThermoCas9 incubated with methylated DNA target with NNNNCCA PAM</name>
        <directory>/data/CC-PAM-methylatedDNA</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>6603</numImagesOrTiltSeries>
        <framesPerImage>50</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 105k magnification using EPU, with a super-resolution pixel size of 0.415 and a  total dose of 60 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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        <name>unaligned multi-frame micrographs of ThermoCas9 incubated with non-methylated DNA target with NNNNCCA PAM</name>
        <directory>/data/CC-PAM-nonmethylatedDNA</directory>
        <category>micrographs - multiframe</category>
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            <pixelWidth>0.415</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.415</pixelHeight>
        </dimensions>
        <details>This dataset was collected on K3 camera at 105k magnification using EPU, with a super-resolution pixel size of 0.415 and a  total dose of 60 spreading over 61 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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        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
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    <imageSet>
        <name>unaligned multi-frame micrographs of ThermoCas9 incubated with non-methylated DNA target with NNNNCGA PAM</name>
        <directory>/data/CG-PAM-nonmethylatedDNA</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>12596</numImagesOrTiltSeries>
        <framesPerImage>50</framesPerImage>
        <voxelType>BIT</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.415</pixelWidth>
            <imageHeight>8184</imageHeight>
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</entry>
