<emd emdb_id="EMD-5923" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-03-13</deposition>
            <header_release>2014-04-09</header_release>
            <map_release>2014-04-09</map_release>
            <update>2014-05-14</update>
        </key_dates>
        <title>Architecture and assembly of the archaeal Cdc48-20S proteasome</title>
        <authors_list>
            <author>Barthelme D</author>
            <author>Chen JZ</author>
            <author>Grabenstatter J</author>
            <author>Baker TA</author>
            <author>Sauer RT</author>
        </authors_list>
        <keywords>Archaeal proteasome, Cdc48, architecture, single-particle EM</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Barthelme D</author>
                    <author order="2">Chen JZ</author>
                    <author order="3">Grabenstatter J</author>
                    <author order="4">Baker TA</author>
                    <author order="5">Sauer RT</author>
                    <title>Architecture and assembly of the archaeal Cdc48*20S proteasome.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>111</volume>
                    <first_page>e1687</first_page>
                    <last_page>e1694</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24711419</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1404823111</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Archaeal proteasome Cdc48-20S</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Archaeal proteasome Cdc48-20S</name>
                <oligomeric_state>One homo-hexamer of Cdc48 binds to one homo-heptamer of 20S</oligomeric_state>
                <number_unique_components>3</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">1.2</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="p97/VCP/VAT">Cdc48</name>
                <natural_source database="NCBI">
                    <organism ncbi="2303">Thermoplasma acidophilum</organism>
                    <strain>DSM 1728</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.5</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21 (DE3)</recombinant_strain>
                    <recombinant_plasmid>pET22b</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">O05209</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>20S alpha subunit</name>
                <natural_source database="NCBI">
                    <organism ncbi="2303">Thermoplasma acidophilum</organism>
                    <strain>DSM 1728</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.36</theoretical>
                </molecular_weight>
                <number_of_copies>7</number_of_copies>
                <oligomeric_state>Heptamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21 (DE3)</recombinant_strain>
                    <recombinant_plasmid>pRSET-A</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P25156</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>20S beta subunit</name>
                <natural_source database="NCBI">
                    <organism ncbi="2303">Thermoplasma acidophilum</organism>
                    <strain>DSM 1728</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.36</theoretical>
                </molecular_weight>
                <number_of_copies>7</number_of_copies>
                <oligomeric_state>Heptamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21 (DE3)</recombinant_strain>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P25156</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">0.023</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>50mM HEPES, 100mM KCl, 20mM MgCl2</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Grids with adsorbed protein floated on 1% w/v uranyl acetate for 15 seconds.</details>
                    </staining>
                    <grid>
                        <details>400 mesh Cu-grid with thin carbon support, glow-discharged before specimen loading</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2100F</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>30000.0</nominal_magnification>
                    <calibrated_magnification>42857.0</calibrated_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">290</temperature_min>
                        <temperature_max units="K">300</temperature_max>
                        <temperature_average units="K">295</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 30,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <details>Weak beam illumination</details>
                    <date>2013-09-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>183</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <details>Every image was 2x-binned before processing.</details>
                            <od_range>1.4</od_range>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were selected manually using the PARTICLE package.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">42.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>PARTICLE</name>
                        </software>
                    </software_list>
                    <number_images_used>4724</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>2612</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1025">
        <file>emd_5923.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>64</col>
            <row>64</row>
            <sec>64</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>64</x>
            <y>64</y>
            <z>64</z>
        </spacing>
        <cell>
            <a units="&#8491;">451.2</a>
            <b units="&#8491;">451.2</b>
            <c units="&#8491;">451.2</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>-4.16351271</minimum>
            <maximum>10.672816279999999</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">7.05</x>
            <y units="&#8491;">7.05</y>
            <z units="&#8491;">7.05</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Single-particle reconstruction of the archaeal Cdc48-20S proteasome</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5923::::</details>
    </map>
</emd>