<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3136" version="3.0.1.1" 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>PDBe</processing_site>
      </current_status>
      <sites>
         <deposition>PDBe</deposition>
         <last_processing>PDBe</last_processing>
      </sites>
      <key_dates>
         <deposition>2015-08-31</deposition>
         <header_release>2015-09-23</header_release>
         <map_release>2015-10-21</map_release>
         <update>2015-10-21</update>
      </key_dates>
      <title>A Single Alpha Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly</title>
      <authors_list>
         <author>Tomko Jr RJ</author>
         <author>Taylor DW</author>
         <author>Chen ZA</author>
         <author>Wang HW</author>
         <author>Rappsilber J</author>
         <author>Hochstrasser M</author>
      </authors_list>
      <keywords>proteasome, ubiquitin, proteolysis, electron microscopy, mass spectrometry</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Tomko RJ</author>
               <author order="2">Taylor DW</author>
               <author order="3">Chen ZA</author>
               <author order="4">Wang HW</author>
               <author order="5">Rappsilber J</author>
               <author order="6">Hochstrasser M</author>
               <title>A Single alpha Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly.</title>
               <journal>CELL(CAMBRIDGE,MASS.)</journal>
               <volume>163</volume>
               <first_page>432</first_page>
               <last_page>444</last_page>
               <year>2015</year>
               <external_references type="PUBMED">26451487</external_references>
               <external_references type="DOI">doi:10.1016/j.cell.2015.09.022</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Recombinant LP2 (Lid Particle 2)</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Recombinant LP2 (Lid Particle 2)</name>
            <details>The sample was monodisperse.</details>
            <oligomeric_state>1 Rpn3: 1 Rpn5: 1 Rpn6: 1 Rpn7: 1 Rpn8: 1 Rpn9: 1 Rpn11: 1 Sem1</oligomeric_state>
            <number_unique_components>8</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.343</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="RPN3">26S proteasome regulatory subunit RPN3</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.064</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P40016</external_references>
               <external_references type="GO">GO:0006511</external_references>
               <external_references type="GO">GO:0042176</external_references>
               <external_references type="GO">GO:0003674</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR013586</external_references>
               <external_references type="INTERPRO">IPR000717</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="RPN5">26S proteasome regulatory subunit RPN5</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.052</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q12250</external_references>
               <external_references type="GO">GO:0006511</external_references>
               <external_references type="GO">GO:0010388</external_references>
               <external_references type="GO">GO:0003674</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR000717</external_references>
               <external_references type="INTERPRO">IPR011991</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="3">
            <name synonym="RPN6">26S proteasome regulatory subunit RPN6</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.050</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q12377</external_references>
               <external_references type="GO">GO:0006511</external_references>
               <external_references type="GO">GO:0005198</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR000717</external_references>
               <external_references type="INTERPRO">IPR013143</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="4">
            <name synonym="RPN7">26S proteasome regulatory subunit RPN7</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.049</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q06103</external_references>
               <external_references type="GO">GO:0006511</external_references>
               <external_references type="GO">GO:0005198</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR019585</external_references>
               <external_references type="INTERPRO">IPR000717</external_references>
               <external_references type="INTERPRO">IPR013026</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="5">
            <name synonym="RPN8">26S proteasome regulatory subunit RPN8</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.038</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q08723</external_references>
               <external_references type="GO">GO:0006511</external_references>
               <external_references type="GO">GO:0003674</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR000555</external_references>
               <external_references type="INTERPRO">IPR024969</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="6">
            <name synonym="RPN9">26S proteasome regulatory subunit RPN9</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.046</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q04062</external_references>
               <external_references type="GO">GO:0006511</external_references>
               <external_references type="GO">GO:0005198</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR000717</external_references>
               <external_references type="INTERPRO">IPR011991</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="7">
            <name synonym="RPN11">26S proteasome regulatory subunit RPN11</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.034</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P43588</external_references>
               <external_references type="GO">GO:0016579</external_references>
               <external_references type="GO">GO:0000266</external_references>
               <external_references type="GO">GO:0004843</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR000555</external_references>
               <external_references type="INTERPRO">IPR024969</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="8">
            <name>26S proteasome regulatory subunit Sem1</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.010</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">O94742</external_references>
               <external_references type="GO">GO:0000502</external_references>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="GO">GO:0043161</external_references>
               <external_references type="GO">GO:0043248</external_references>
               <external_references type="INTERPRO">IPR007834</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">0.04</concentration>
               <buffer>
                  <ph>7.5</ph>
                  <details>50 mM Tris, 150 mM NaCl, 5 mM MgCl2, and 10% glycerol</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Sample was negatively stained with six consecutive droplets of 2% uranyl acetate.</details>
               </staining>
               <grid>
                  <details>400 mesh Cu grid with thin carbon, glow discharged with a sputter coater.</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>FEI TECNAI 20</microscope>
               <illumination_mode>FLOOD BEAM</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>FIELD EMISSION GUN</electron_source>
               <acceleration_voltage units="kV">120</acceleration_voltage>
               <nominal_cs units="mm">2.2</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">1.4</nominal_defocus_max>
               <nominal_magnification>80000.0</nominal_magnification>
               <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
               <details>Data acquired using Leginon.</details>
               <date>2013-04-26</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                     <number_real_images>600</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Each micrograph</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">16.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN2, SPARX</name>
                  </software>
               </software_list>
               <number_images_used>60000</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="16001">
      <file>emd_3136.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>160</col>
         <row>160</row>
         <sec>160</sec>
      </dimensions>
      <origin>
         <col>-80</col>
         <row>-80</row>
         <sec>-80</sec>
      </origin>
      <spacing>
         <x>160</x>
         <y>160</y>
         <z>160</z>
      </spacing>
      <cell>
         <a units="&#8491;">448.0</a>
         <b units="&#8491;">448.0</b>
         <c units="&#8491;">448.0</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>-19.906469349999998</minimum>
         <maximum>23.58402061</maximum>
         <average>0.0</average>
         <std>0.99999994</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.8</x>
         <y units="&#8491;">2.8</y>
         <z units="&#8491;">2.8</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>5.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of LP2</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3136::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_3136.png</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>