<?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_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-8341">
    <admin>
        <current_status>
            <date>2024-10-09</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-08-16</deposition>
            <header_release>2016-08-31</header_release>
            <map_release>2016-08-31</map_release>
            <update>2024-10-09</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute on Aging (NIH/NIA)</funding_body>
                <code>AG15709-19</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Sub-Complex Formed by the Iron Donor, Yfh1, and the Scaffold, Isu1</title>
        <authors_list>
            <author>Ranatunga W</author>
            <author>Gakh O</author>
        </authors_list>
        <keywords>Friedreich Ataxia, frataxin, iron-sulfur protein, mitochondria, protein complex, OXIDOREDUCTASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Ranatunga W</author>
                    <author order="2">Gakh O</author>
                    <author order="3">Galeano BK</author>
                    <author order="4">Smith IV DY</author>
                    <author order="5">Soderberg CA</author>
                    <author order="6">Al-Karadaghi S</author>
                    <author order="7">Thompson JR</author>
                    <author order="8">Isaya G</author>
                    <title>Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Sub-Complex Formed by the Iron Donor, Yfh1, and the Scaffold, Isu1</title>
                    <journal_abbreviation>J. Biol. Chem.</journal_abbreviation>
                    <country>US</country>
                    <volume>291</volume>
                    <first_page>10378</first_page>
                    <last_page>10398</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26941001</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M115.712414</external_references>
                    <external_references type="ISSN">0021-9258</external_references>
                    <external_references type="CSD">0071</external_references>
                    <external_references type="ASTM">JBCHA3</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8301</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5t0v</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Yfh1-Isu1</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Yfh1-Isu1</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>macromolecule comprising 24-mer of Yfh1 and 24-mer of Isu1</details>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.7</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Iron sulfur cluster assembly protein 1, mitochondrial</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.015383871999999998</theoretical>
                </molecular_weight>
                <number_of_copies>24</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="1354003">Escherichia coli #1/H766</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>GSHMSSITKRLYHPKVIEHYTHPRNVGSLDKKLPNVGTGLVGAPACGDVMRLQIKVNDSTGVIEDVKFKTFGCGSAIASS
SYMTELVQGMTLDDAAKIKNTEIAKELSLPPVKLHCSMLAEDAIKAAIKDYKSKRNTPTMLS</string>
                    <external_references type="UNIPROTKB">Q03020</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Frataxin homolog, mitochondrial</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.013455976</theoretical>
                </molecular_weight>
                <number_of_copies>24</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="1354003">Escherichia coli #1/H766</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>VESSTDGQVVPQEVLNLPLEKAHEEADDYLDHLLDSLEELSEAHPDCIPDVELSHGVMTLEIPAFGTYVINKQPPNKQIW
LASPLSGPNRFDLLNGEWVSLRNGTKLTDILTEEVEKAISK</string>
                    <external_references type="UNIPROTKB">Q07540</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">0.12</concentration>
                    <buffer>
                        <ph>7.3</ph>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <formula>C8H19KN2O5S</formula>
                            <name>HEPES-KOH</name>
                        </component>
                        <component>
                            <concentration units="mM">100.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>uranyl acetate</material>
                        <details>Pre-incubated in HN100 buffer, the grid was placed on an 11-microliter drop of protein sample for 1 minute. Excess protein sample was blotted and washed for 3 seconds by placing the grid on a drop of sterile water. After excess water was blotted, the grid was stained with 1% w/v uranyl acetate for 1 second and 30 seconds by successively placing it on two separate drops of uranyl acetate, with excess stain drawn off after each step.</details>
                    </staining>
                    <grid>
                        <model>carbon-coated, EMS</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                        </pretreatment>
                        <details>DV-502A instrument, Denton Vacuum Inc.</details>
                    </grid>
                    <details>The protein complex was prepared by incubating Yfh1 and Isu1 (1:1.5 molar ratio) in HN100 buffer (10 mM HEPES-KOH, pH 7.3, 100 mM NaCl) and purified using Sephacryl S300 gel filtration chromatography.</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</microscope>
                    <illumination_mode>OTHER</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">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">0.21</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">0.21</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">2.8000000000000003</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">2.8000000000000003</calibrated_defocus_max>
                    <nominal_magnification>115000.0</nominal_magnification>
                    <calibrated_magnification>115000.0</calibrated_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>559</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">30.0</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>
                <details>432 symmetry applied for reconstruction</details>
                <particle_selection>
                    <number_selected>4153</number_selected>
                </particle_selection>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>O</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">17.5</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.06</version>
                        </software>
                    </software_list>
                    <number_images_used>4153</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="95552">
        <file>emd_8341.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>288</col>
            <row>288</row>
            <sec>288</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>288</x>
            <y>288</y>
            <z>288</z>
        </spacing>
        <cell>
            <a units="Å">297.79202</a>
            <b units="Å">297.79202</b>
            <c units="Å">297.79202</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>-8.725704</minimum>
            <maximum>12.439627</maximum>
            <average>0.042547934</average>
            <std>0.8003871</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.034</x>
            <y units="Å">1.034</y>
            <z units="Å">1.034</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.8</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8341::::</label>
        <annotation_details>Yfh1_Isu1 sub-complex</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
