<?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_11_0/emdb.xsd" version="3.0.11.0" emdb_id="EMD-54657">
    <admin composite_map="true">
        <current_status>
            <date>2025-12-03</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2025-08-05</deposition>
            <header_release>2025-11-12</header_release>
            <map_release>2025-11-12</map_release>
            <update>2025-12-03</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Max Planck Society</funding_body>
                <country>Germany</country>
            </grant_reference>
            <grant_reference>
                <funding_body>European Research Council (ERC)</funding_body>
                <code>101054823</code>
                <country>European Union</country>
            </grant_reference>
            <grant_reference>
                <funding_body>European Molecular Biology Organization (EMBO)</funding_body>
                <code>ALTF 33-2021</code>
                <country>European Union</country>
            </grant_reference>
        </grant_support>
        <title>Composite map of the A. thaliana nuclera pore complex</title>
        <authors_list>
            <author>Sanchez Carrillo IB</author>
            <author ORCID="0000-0003-3421-6363">Hoffmann PC</author>
            <author ORCID="0000-0001-7686-695X">Obarska-Kosinska A</author>
            <author>Fourcassie V</author>
            <author ORCID="0000-0002-7397-1321">Beck M</author>
            <author>Germain H</author>
        </authors_list>
        <keywords>nuclear pore complex, NUCLEAR PROTEIN, MEMBRANE PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-7711-9603" order="1">Sanchez Carrillo IB</author>
                    <author ORCID="0000-0003-3421-6363" order="2">Hoffmann PC</author>
                    <author order="3">Obarska-Kosinska A</author>
                    <author ORCID="0009-0003-7232-5314" order="4">Fourcassie V</author>
                    <author ORCID="0000-0002-7397-1321" order="5">Beck M</author>
                    <author ORCID="0000-0002-7046-6194" order="6">Germain H</author>
                    <title>In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana.</title>
                    <journal_abbreviation>Nat.Plants</journal_abbreviation>
                    <country>UK</country>
                    <volume>11</volume>
                    <first_page>2368</first_page>
                    <last_page>2380</last_page>
                    <year>2025</year>
                    <external_references type="PUBMED">41174229</external_references>
                    <external_references type="DOI">doi:10.1038/s41477-025-02138-y</external_references>
                    <external_references type="ISSN">2055-0278</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-54653</emdb_id>
                <relationship>
                    <other>consensus EM volume</other>
                </relationship>
                <details>asymmetric subunit STA map</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-54654</emdb_id>
                <relationship>
                    <other>focused EM volume</other>
                </relationship>
                <details>focused map IR</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-54655</emdb_id>
                <relationship>
                    <other>focused EM volume</other>
                </relationship>
                <details>focused map CR</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-54656</emdb_id>
                <relationship>
                    <other>focused EM volume</other>
                </relationship>
                <details>focused map NR</details>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>9sob</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-54653</accession_id>
                <content_type>consensus EM volume</content_type>
                <details>asymmetric subunit STA map</details>
            </db_reference>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-54654</accession_id>
                <content_type>focused EM volume</content_type>
                <details>focused map IR</details>
            </db_reference>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-54655</accession_id>
                <content_type>focused EM volume</content_type>
                <details>focused map CR</details>
            </db_reference>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-54656</accession_id>
                <content_type>focused EM volume</content_type>
                <details>focused map NR</details>
            </db_reference>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-54657</accession_id>
                <content_type>associated EM volume</content_type>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Nuclear pore complex</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Nuclear pore complex</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="3702">Arabidopsis thaliana</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>5.7</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                    <details>Cryo-FIB lamellae of isolated A.thaliana root protoplasts</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>TFS 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">2.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 BIOQUANTUM (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">2.2</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">33.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>novaSTA</name>
                        </software>
                    </software_list>
                    <details>composite map</details>
                    <number_subtomograms_used>632</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>37</number_tomograms>
                    <number_images_used>79</number_images_used>
                    <software_list>
                        <software>
                            <name>novaSTA</name>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <type>PHASE FLIPPING ONLY</type>
                </ctf_correction>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32001">
        <file>emd_54657.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">1740.8</a>
            <b units="Å">1740.8</b>
            <c units="Å">1740.8</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>-0.33343223</minimum>
            <maximum>0.38045403</maximum>
            <average>0.0027647496</average>
            <std>0.025010884</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">8.704</x>
            <y units="Å">8.704</y>
            <z units="Å">8.704</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.07</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-54657::::</label>
        <annotation_details>Composite NPC map</annotation_details>
    </map>
</emd>
