<?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_2/emdb.xsd" version="3.0.9.2" emdb_id="EMD-6830">
    <admin>
        <current_status>
            <date>2024-03-27</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-10-02</deposition>
            <header_release>2017-04-19</header_release>
            <map_release>2018-02-21</map_release>
            <update>2024-03-27</update>
        </key_dates>
        <title>human ferritin mutant - E-helix deletion</title>
        <authors_list>
            <author>Lee SG</author>
            <author>Yoon HR</author>
        </authors_list>
        <keywords>ferritin, cage, drug delivery, TRANSPORT PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Ahn B</author>
                    <author order="2">Lee SG</author>
                    <author order="3">Yoon HR</author>
                    <author order="4">Lee JM</author>
                    <author order="5">Oh HJ</author>
                    <author order="6">Kim HM</author>
                    <author order="7">Jung Y</author>
                    <title>Four-fold Channel-Nicked Human Ferritin Nanocages for Active Drug Loading and pH-Responsive Drug Release</title>
                    <journal_abbreviation>Angew. Chem. Int. Ed. Engl.</journal_abbreviation>
                    <country>GE</country>
                    <volume>57</volume>
                    <first_page>2909</first_page>
                    <last_page>2913</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">29359486</external_references>
                    <external_references type="DOI">doi:10.1002/anie.201800516</external_references>
                    <external_references type="ISSN">1521-3773</external_references>
                    <external_references type="CSD">0179</external_references>
                    <external_references type="ASTM">ACIEAY</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-6714</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5yi5</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>human ferritin E-helix deletion mutant</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>human ferritin E-helix deletion mutant</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.42</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Ferritin heavy chain</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.020608104999999998</theoretical>
                </molecular_weight>
                <number_of_copies>24</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGR
IFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMG
APESGLAEYLFDKHTLG</string>
                    <external_references type="UNIPROTKB">P02794</external_references>
                </sequence>
                <ec_number>1.16.3.1</ec_number>
            </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">0.05</concentration>
                    <buffer>
                        <ph>7.2</ph>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>Tris</formula>
                            <name>tris(hydroxymethyl)aminomethane</name>
                        </component>
                        <details>buffers were titrated with HCl to pH7.2</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <support_film film_type_id="2">
                            <film_material>GRAPHENE OXIDE</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                            <atmosphere>AIR</atmosphere>
                            <pressure units="kPa">0.039</pressure>
                        </pretreatment>
                        <details>the grid was coated with graphene oxide prior to use</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">276</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>blot for 9 seconds before plunging. </details>
                    </vitrification>
                    <details>this sample was monodisperse</details>
                </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_cs units="mm">0.002</nominal_cs>
                    <nominal_magnification>47000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <frames_per_image>2-29</frames_per_image>
                            </digitization_details>
                            <average_exposure_time units="s">1.8</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">2.0</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>
                <particle_selection>
                    <number_selected>623510</number_selected>
                </particle_selection>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>4Y08</pdb_id>
                    </pdb_model>
                    <details>human ferritin</details>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <details>relion2.0 program was used for the reconstruction</details>
                    <number_images_used>429135</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8389">
        <file>emd_6830.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>128</col>
            <row>128</row>
            <sec>128</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="Å">178.8544</a>
            <b units="Å">178.8544</b>
            <c units="Å">178.8544</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>-0.45643964</minimum>
            <maximum>0.88335246</maximum>
            <average>0.021175088</average>
            <std>0.08361874</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.3973</x>
            <y units="Å">1.3973</y>
            <z units="Å">1.3973</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.3</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-6830::::</label>
        <annotation_details>human ferritin heavy chain complexed with doxorubicin</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4Y08</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                        <residue_range>5-160</residue_range>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>29.559999999999999</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
