<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_8/emdb.xsd" emdb_id="EMD-0722" version="3.0.1.8">
    <admin>
        <current_status>
            <date>2020-04-15</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-07-30</deposition>
            <header_release>2020-04-15</header_release>
            <map_release>2020-04-15</map_release>
            <update>2020-04-15</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Natural Science Foundation of China</funding_body>
                <code>31770794</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Ministry of Science and Technology (China)</funding_body>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Chinese Academy of Sciences</funding_body>
                <code>XDB08030202</code>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>Full length S-OPA1 coated liposome tube at nucleotide-free state</title>
        <authors_list>
            <author>Zhang D</author>
            <author>Niu T</author>
            <author>Zhang Y</author>
            <author>Sun F</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang D</author>
                    <author order="2">Zhang Y</author>
                    <author order="3">Ma J</author>
                    <author order="4">Zhu C</author>
                    <author order="5">Niu T</author>
                    <author order="6">Chen W</author>
                    <author order="7">Pang X</author>
                    <author order="8">Zhai Y</author>
                    <author order="9">Sun F</author>
                    <title>Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding.</title>
                    <journal_abbreviation>Elife</journal_abbreviation>
                    <country>US</country>
                    <volume>9</volume>
                    <year>2020</year>
                    <external_references type="PUBMED">32228866</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.50294</external_references>
                    <external_references type="ISSN">2050-084X</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0722</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>full length S-OPA1 coated liposome tube</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>full length S-OPA1 coated liposome tube</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>1mg/ml full length S-OPA1 was incubated with 1mg/ml liposome at room temperature for 30 min.</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Dynamin-like 120 kDa protein, mitochondrial, short form for isoform 1, Optic atrophy protein 1 (OPA1), short form for isoform 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>GPGSTDRGSESDKHFRKVSDKEKIDQLQEELLHTQLKYQRILERLEKEN
KELRKLVLQKDDKGIHHRKLKKSLIDMYSEVLDVLSDYDASYNTQDHLPRVVVVGDQSAG
KTSVLEMIAQARIFPRGSGEMMTRSPVKVTLSEGPHHVALFKDSSREFDLTKEEDLAALR
HEIELRMRKNVKEGCTVSPETISLNVKGPGLQRMVLVDLPGVINTVTSGMAPDTKETIFS
ISKAYMQNPNAIILCIQDGSVDAERSIVTDLVSQMDPHGRRTIFVLTKVDLAEKNVASPS
RIQQIIEGKLFPMKALGYFAVVTGKGNSSESIEAIREYEEEFFQNSKLLKTSMLKAHQVT
TRNLSLAVSDCFWKMVRESVEQQADSFKATRFNLETEWKNNYPRLRELDRNELFEKAKNE
ILDEVISLSQVTPKHWEEILQQSLWERVSTHVIENIYLPAAQTMNSGTFNTTVDIKLKQW
TDKQLPNKAVEVAWETLQEEFSRFMTEPKGKEHDDIFDKLKEAVKEESIKRHKWNDFAED
SLRVIQHNALEDRSISDKQQWDAAIYFMEEALQARLKDTENAIENMVGPDWKKRWLYWKN
RTQEQCVHNETKNELEKMLKCNEEHPAYLASDEITTVRKNLESRGVEVDPSLIKDTWHQV
YRRHFLKTALNHCNLCRRGFYYYQRHFVDSELECNDVVLFWRIQRMLAITANTLRQQLTN
TEVRRLEKNVKEVLEDFAEDGEKKIKLLTGKRVQLAEDLKKVREIQEKLDAFIEALHQEK</string>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <concentration units="mg/mL">1</concentration>
                    <buffer>
                        <ph>8</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Tris</formula>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>MgCl2</formula>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>EGTA</formula>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/1</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>OTHER</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">289</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>The grid was blotted for 3.5s with force 1 before plunging.. </details>
                    </vitrification>
                    <details>1mg/ml full length S-OPA1 was incubated with 1mg/ml liposome at room temperature for 30 min.</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">4.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3838</width>
                                    <height units="pixel">3710</height>
                                </dimensions>
                                <frames_per_image>1-12</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <average_exposure_time units="s">1.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">3.0</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>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">31.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                    <number_subtomograms_used>436</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>9</number_tomograms>
                    <number_images_used>773</number_images_used>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                            <version>4.2.9</version>
                        </software>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>4</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8389">
        <file>emd_0722.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>-64</col>
            <row>-64</row>
            <sec>-64</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="Å">348.16</a>
            <b units="Å">348.16</b>
            <c units="Å">348.16</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>-0.23188168</minimum>
            <maximum>0.29639256</maximum>
            <average>0.008297293</average>
            <std>0.05131582</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.72</x>
            <y units="Å">2.72</y>
            <z units="Å">2.72</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.07</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0722::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3SNH</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
