<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-11745" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2023-08-03</depositionDate>
            <releaseDate>2024-06-04</releaseDate>
            <updateDate>2024-06-04</updateDate>
        </keyDates>
        <title>In vitro TDP-43 amyloid fibrils</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-9442-460X</authorORCID>
            <firstName>Matthias</firstName>
            <lastName>Schmidt</lastName>
            <organization type="academic">Institut für Proteinbiochemie, Universität Ulm</organization>
            <street>Helmholtzstrasse 8/1</street>
            <townOrCity>Ulm</townOrCity>
            <stateOrProvince>Baden Württemberg</stateOrProvince>
            <country>Germany</country>
            <postOrZipCode>89081</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0003-2123-6816</authorORCID>
            <firstName>Marcus</firstName>
            <lastName>Fändrich</lastName>
            <organization type="academic">Institut für Proteinbiochemie, Universität Ulm</organization>
            <street>Helmholtzstrasse 8/1</street>
            <townOrCity>Ulm</townOrCity>
            <stateOrProvince>Baden Württemberg</stateOrProvince>
            <country>Germany</country>
            <postOrZipCode>89081</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0003-3375-7168">Sharma K</author>
            <author authorORCID="0000-0002-9442-460X">Schmidt M</author>
            <author authorORCID="0000-0003-2123-6816">Fändrich M</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody></fundingBody>
                <code></code>
                <country></country>
            </grantReference>
        </grantSupport>
        <datasetSize units="GB">280.1</datasetSize>
        <entryDOI>10.6019/EMPIAR-11745</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>molecule</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-18715</emdbEntry>
            <emdbEntry>EMD-18716</emdbEntry>
            <emdbEntry>EMD-18717</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0003-3375-7168" order="1">Sharma K</author>
                    <author authorORCID="0009-0009-2685-4390" order="2">Stockert F</author>
                    <author authorORCID="0000-0002-0360-645X" order="3">Shenoy J</author>
                    <author order="4">Berbon M</author>
                    <author order="5">Abdul-Shukkoor MB</author>
                    <author authorORCID="0000-0003-3723-9552" order="6">Habenstein B</author>
                    <author authorORCID="0000-0001-7176-7813" order="7">Loquet A</author>
                    <author authorORCID="0000-0002-9442-460X" order="8">Schmidt M</author>
                    <author authorORCID="0000-0003-2123-6816" order="9">Fändrich M</author>
                    <title>Cryo-EM observation of the amyloid key structure of polymorphic TDP-43 amyloid fibrils</title>
                    <journal>Nature communications</journal>
                    <journalAbbreviation>Nat Commun</journalAbbreviation>
                    <country></country>
                    <issue>1</issue>
                    <volume>15</volume>
                    <year>2024</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1038/s41467-023-44489-0</externalReferences>
                    <externalReferences type="pubmed">38212334</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Unaligned multi-frame micrographs of TDP-43 amyloid fibrils</name>
        <directory>/data/EM_data</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>1641</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>3838</imageWidth>
            <pixelWidth>1.04</pixelWidth>
            <imageHeight>3710</imageHeight>
            <pixelHeight>1.04</pixelHeight>
        </dimensions>
        <details>The gain reference (/data/EM_data/CountRef_0001.dm4) is not applied to the raw micrographs. The NOTES.txt file contains EM information (copied below). The coordinates are divided into Morphology-1 (/data/Coordinatesfiles_Morphology1) and Morphology-2 (/data/Coordinatesfiles_Morphology2).

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
NOTES.txt 

EMBL Heidelberg
Krios1 Quantum-K2
Cs 2.7
300kV EFTEM nanpprobe
x130k spot 8 beam size 650nm
c2=50  objective_aperture=100

GIF-K2 counting
10s exposure 40 frames
total dose at the sample 52.08e/A2
1 pixel = 1.04A
dose rate ~3-4 e/pix/s

defocus range -1.2 to -2.5</details>
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        <micrographsFilePattern>data/EM_data/*.tif</micrographsFilePattern>
        <pickedParticlesFilePattern>data/Coordinatesfiles_Morphology*/*_manualpick.star</pickedParticlesFilePattern>
        <pickedParticlesDirectory>data/Coordinatesfiles_Morphology*</pickedParticlesDirectory>
    </imageSet>
</entry>
