<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-13331" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2025-11-06</depositionDate>
            <releaseDate>2026-04-09</releaseDate>
            <updateDate>2026-04-09</updateDate>
        </keyDates>
        <title>Cryo electron tomography of BG505 HIV-1 Env in a virus-like particle</title>
        <correspondingAuthor private="true">
            <authorORCID>0009-0001-4737-542X</authorORCID>
            <firstName>Madeleine</firstName>
            <middleName>Camille</middleName>
            <lastName>Duquette</lastName>
            <organization type="academic">UC San Diego</organization>
            <street>9500 Gilman Drive</street>
            <townOrCity>La Jolla</townOrCity>
            <stateOrProvince>CA</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>92093</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0003-4677-9809</authorORCID>
            <firstName>Elizabeth</firstName>
            <lastName>Villa</lastName>
            <organization type="academic">Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA</organization>
            <street>9500 Gilman Drive</street>
            <townOrCity>La Jolla</townOrCity>
            <stateOrProvince>CA</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>92093</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0009-0001-4737-542X">Duquette MC</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</fundingBody>
                <code>U54 AI170856</code>
                <country>United States</country>
            </grantReference>
        </grantSupport>
        <datasetSize units="GB">963.0</datasetSize>
        <entryDOI>10.6019/EMPIAR-13331</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>virus</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-75641</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="true">
                    <author authorORCID="0000-0003-0841-4577" order="1">Shehata M</author>
                    <author authorORCID="0000-0003-3581-1148" order="2">Casalino L</author>
                    <author authorORCID="0009-0001-4737-542X" order="3">Duquette M</author>
                    <author authorORCID="0000-0003-4565-4772" order="4">Chen S</author>
                    <author authorORCID="0009-0001-2779-2082" order="5">Flaherty A</author>
                    <author authorORCID="0000-0003-4677-9809" order="6">Villa E</author>
                    <author authorORCID="0000-0002-9275-9553" order="7">Amaro RE</author>
                    <title>N-Glycans Modulate HIV-1 Env Conformational Plasticity</title>
                    <journal>bioRxiv</journal>
                    <journalAbbreviation></journalAbbreviation>
                    <country>United States</country>
                    <year>2025</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1101/2025.03.26.645577</externalReferences>
                    <details>The micrographs were collected on a Titan Krios G4 TEM (Thermo Fisher) operating at 300 Kv with a Falcon 4i direct electron detector (Thermo Fisher) at a nominal magnification of 81,000x (pixel size 1.561 Å, counting mode). A Selectris X energy filter with a 10 eV-wide slit was used throughout data collection. PaceTOMO was used to collect tilt series. 224 EER frames were collected per tilt series at a dose rate of 4.4 e-/Å2/s.  The raw EER frames are provided, as well as the mdocs.</details>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Raw cryoET data from collection on 7/18/2025</name>
        <directory>/data/Dataset1_frames</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>EER</headerFormat>
        <dataFormat>EER</dataFormat>
        <numImagesOrTiltSeries>4012</numImagesOrTiltSeries>
        <framesPerImage>224</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>4096</imageWidth>
            <pixelWidth>1.561</pixelWidth>
            <imageHeight>4096</imageHeight>
            <pixelHeight>1.561</pixelHeight>
        </dimensions>
        <details>There are 224 EER frames per image, and each tilt series is comprised of up to 37 tilts. Some of them have fewer tilts because the stage has a maximum tilt angle and some of the targets had a larger estimated pre-tilt while setting up paceTOMO. Associated metadata from SerialEM is in the mdocs folder.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Raw cryoET data from collection on 7/19/2025</name>
        <directory>/data/Dataset2_frames</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>EER</headerFormat>
        <dataFormat>EER</dataFormat>
        <numImagesOrTiltSeries>5884</numImagesOrTiltSeries>
        <framesPerImage>224</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>4096</imageWidth>
            <pixelWidth>1.561</pixelWidth>
            <imageHeight>4096</imageHeight>
            <pixelHeight>1.561</pixelHeight>
        </dimensions>
        <details>There are 224 EER frames per image, and each tilt series is comprised of up to 37 tilts. Some of them have fewer tilts because the stage has a maximum tilt angle and some of the targets had a larger estimated pre-tilt while setting up paceTOMO. Associated metadata from SerialEM is in the mdocs folder.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
