<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_1/emdb.xsd" version="3.0.9.1" emdb_id="EMD-28929">
    <admin>
        <current_status>
            <date>2024-01-17</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-11-21</deposition>
            <header_release>2023-03-22</header_release>
            <map_release>2023-03-22</map_release>
            <update>2024-01-17</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains - KWOCA51</title>
        <authors_list>
            <author ORCID="0000-0003-4297-7824">Borst AJ</author>
            <author>King NP</author>
        </authors_list>
        <keywords>tetradron, KWOCA, secretable, DE NOVO PROTEIN, design, degreaser, cage, vaccine</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-1511-6976" order="1">Wang JYJ</author>
                    <author order="2">Khmelinskaia A</author>
                    <author order="3">Sheffler W</author>
                    <author order="4">Miranda MC</author>
                    <author order="5">Antanasijevic A</author>
                    <author ORCID="0000-0003-4297-7824" order="6">Borst AJ</author>
                    <author ORCID="0000-0001-8226-8227" order="7">Torres SV</author>
                    <author order="8">Shu C</author>
                    <author ORCID="0000-0001-7467-8373" order="9">Hsia Y</author>
                    <author order="10">Nattermann U</author>
                    <author order="11">Ellis D</author>
                    <author order="12">Walkey C</author>
                    <author order="13">Ahlrichs M</author>
                    <author ORCID="0000-0002-1617-0464" order="14">Chan S</author>
                    <author ORCID="0000-0001-5487-0499" order="15">Kang A</author>
                    <author ORCID="0000-0001-9696-4004" order="16">Nguyen H</author>
                    <author order="17">Sydeman C</author>
                    <author order="18">Sankaran B</author>
                    <author order="19">Wu M</author>
                    <author order="20">Bera AK</author>
                    <author ORCID="0000-0002-9837-9068" order="21">Carter L</author>
                    <author ORCID="0000-0003-0148-5268" order="22">Fiala B</author>
                    <author order="23">Murphy M</author>
                    <author ORCID="0000-0001-7896-6217" order="24">Baker D</author>
                    <author ORCID="0000-0001-7153-3769" order="25">Ward AB</author>
                    <author ORCID="0000-0002-2978-4692" order="26">King NP</author>
                    <title>Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains.</title>
                    <journal_abbreviation>Proc.Natl.Acad.Sci.USA</journal_abbreviation>
                    <country>US</country>
                    <volume>120</volume>
                    <first_page>e2214556120</first_page>
                    <last_page>e2214556120</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">36888664</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.2214556120</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>KWOCA51</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>KWOCA51</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>KWOCA51</name>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>METDTLLLWVLLLWVPGSTGDGSHHHHHHGGSEQKLISEEDLSGGGSWSGSSDEEEAREWAERAEEAAKEALEQAKREGDEIARLCAKMLEILAEEARRKKDSEEAEAVYWAARAVLAALEALEQAKREGDEDARRCAEELLRLACSAAARQDSEQARAVYEAARAVLAALRALEAAKRAGMEEARKEAEELLRRACEAARKQDPELARAVRDKAELLKALADLFKALKELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKIIVEVLRIIAEVLRINARAV</string>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">3.0</concentration>
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_defocus_min units="µm">-0.7000000000000001</nominal_defocus_min>
                    <nominal_defocus_max units="µm">-1.8</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">65.476</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <startup_model type_of_model="OTHER">
                    <details>Ab initio 3D - cryosparc</details>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">5.87</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>397630</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="186625">
        <file>emd_28929.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>360</col>
            <row>360</row>
            <sec>360</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>360</x>
            <y>360</y>
            <z>360</z>
        </spacing>
        <cell>
            <a units="Å">302.4</a>
            <b units="Å">302.4</b>
            <c units="Å">302.4</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.30373022</minimum>
            <maximum>0.5903399</maximum>
            <average>-0.0023801876</average>
            <std>0.02469611</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.84</x>
            <y units="Å">0.84</y>
            <z units="Å">0.84</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.161</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-28929::::</label>
        <annotation_details>Unsharpened Map</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="186625">
                <file>emd_28929_additional_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>360</col>
                    <row>360</row>
                    <sec>360</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>360</x>
                    <y>360</y>
                    <z>360</z>
                </spacing>
                <cell>
                    <a units="Å">302.4</a>
                    <b units="Å">302.4</b>
                    <c units="Å">302.4</c>
                    <alpha units="deg">90.0</alpha>
                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
                </cell>
                <axis_order>
                    <fast>X</fast>
                    <medium>Y</medium>
                    <slow>Z</slow>
                </axis_order>
                <statistics>
                    <minimum>-0.65553725</minimum>
                    <maximum>1.0168756</maximum>
                    <average>-0.0015328265</average>
                    <std>0.033718444</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.84</x>
                    <y units="Å">0.84</y>
                    <z units="Å">0.84</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28929::::</label>
                <annotation_details>Sharpened Map</annotation_details>
            </additional_map>
        </additional_map_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="186625">
                <file>emd_28929_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>360</col>
                    <row>360</row>
                    <sec>360</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>360</x>
                    <y>360</y>
                    <z>360</z>
                </spacing>
                <cell>
                    <a units="Å">302.4</a>
                    <b units="Å">302.4</b>
                    <c units="Å">302.4</c>
                    <alpha units="deg">90.0</alpha>
                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
                </cell>
                <axis_order>
                    <fast>X</fast>
                    <medium>Y</medium>
                    <slow>Z</slow>
                </axis_order>
                <statistics>
                    <minimum>-0.50498927</minimum>
                    <maximum>0.69094646</maximum>
                    <average>0.00025285</average>
                    <std>0.05941129</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.84</x>
                    <y units="Å">0.84</y>
                    <z units="Å">0.84</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28929::::</label>
                <annotation_details>Half Map A</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="186625">
                <file>emd_28929_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>360</col>
                    <row>360</row>
                    <sec>360</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>360</x>
                    <y>360</y>
                    <z>360</z>
                </spacing>
                <cell>
                    <a units="Å">302.4</a>
                    <b units="Å">302.4</b>
                    <c units="Å">302.4</c>
                    <alpha units="deg">90.0</alpha>
                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
                </cell>
                <axis_order>
                    <fast>X</fast>
                    <medium>Y</medium>
                    <slow>Z</slow>
                </axis_order>
                <statistics>
                    <minimum>-0.47281483</minimum>
                    <maximum>0.6825893</maximum>
                    <average>0.0002594447</average>
                    <std>0.059414607</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.84</x>
                    <y units="Å">0.84</y>
                    <z units="Å">0.84</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28929::::</label>
                <annotation_details>Half Map B</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
