<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-3273" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-12-08</deposition>
            <header_release>2015-12-16</header_release>
            <obsolete>2016-10-05</obsolete>
            <update>2016-10-05</update>
        </key_dates>
        <title>Human mithocondrial Lon protease lacking the first 271 amino acids.</title>
        <authors_list>
            <author>Kereiche S</author>
            <author>Kovacik L</author>
            <author>Kutejova E</author>
            <author>Bednar J</author>
            <author>Pevala V</author>
            <author>Ambro L</author>
            <author>Bellova J</author>
            <author>Raska I</author>
        </authors_list>
        <keywords>AAA, Lon protease, Human</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Kereiche S</author>
                    <author order="2">Kovacik L</author>
                    <author order="3">Kutejova E</author>
                    <author order="4">Bednar J</author>
                    <author order="5">Pevala V</author>
                    <author order="6">Ambro L</author>
                    <author order="7">Bellova J</author>
                    <author order="8">Raska I</author>
                    <title>Conformational change of Human mitochondrial Lon protease</title>
                    <journal>NAT.STRUCT.BIOL.</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Human mitochondrial Lon protease D271</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Human mitochondrial Lon protease D271</name>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.43</experimental>
                    <theoretical units="MDa">0.43</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="LonP1">human Lon protease</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                    <organelle>mitochondria</organelle>
                    <cellular_location>mitochondria</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.43</experimental>
                    <theoretical units="MDa">0.43</theoretical>
                </molecular_weight>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>DE3</recombinant_strain>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P36776</external_references>
                </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">1</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>20 mM HEPES, 150 mM NaCl, 5 mM MgCl2</details>
                    </buffer>
                    <grid>
                        <details>200 mesh quanti-foil R2/2 with thin carbon support, glow discharged in standard vaccum atmosphere</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>blot 2 seconds before plunging</method>
                    </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_cs units="mm">0</nominal_cs>
                    <nominal_defocus_min units="µm">1.3</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.4</nominal_defocus_max>
                    <nominal_magnification>47000.0</nominal_magnification>
                    <calibrated_magnification>98682.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2014-04-04</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="µm">14</sampling_interval>
                            </digitization_details>
                            <number_real_images>2980</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">10</average_electron_dose_per_image>
                            <bits_per_pixel>16.0</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>ctffind3</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">20.9</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>39800</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>20</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="27649">
        <file>emd_3273.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>192</col>
            <row>192</row>
            <sec>192</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>192</x>
            <y>192</y>
            <z>192</z>
        </spacing>
        <cell>
            <a units="Å">272.63998</a>
            <b units="Å">272.63998</b>
            <c units="Å">272.63998</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>-0.02581789</minimum>
            <maximum>0.0574743</maximum>
            <average>0.00040323</average>
            <std>0.005783</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.42</x>
            <y units="Å">1.42</y>
            <z units="Å">1.42</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0205</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the Human Lon protease lacking the first 271 amino acids.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3273::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3M6A</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>sculptor, situs, Chimera</name>
                    </software>
                </software_list>
                <details>The domains were separately fitted by interactive docking in the situs programme. Only five copies could be fitted.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_3273.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>
