<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3405" 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>2016-03-30</deposition>
         <header_release>2016-05-04</header_release>
         <map_release>2017-08-02</map_release>
         <update>2017-08-02</update>
      </key_dates>
      <title>Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle</title>
      <authors_list>
         <author>Carter SD</author>
         <author>Hampton CM</author>
         <author>Langlois R</author>
         <author>Grassucci RA</author>
         <author>Farino ZJ</author>
         <author>Morgenstern TM</author>
         <author>Rice WJ</author>
         <author>Velasco KR</author>
         <author>Wigge C</author>
         <author>Xu Y</author>
         <author>Koller A</author>
         <author>Melero R</author>
         <author>Mitchell WG</author>
         <author>Yi E</author>
         <author>Aguilar JI</author>
         <author>Levy ES</author>
         <author>Greenberg NL</author>
         <author>Li W</author>
         <author>Courel M</author>
         <author>Mahata SK</author>
         <author>Freyberg R</author>
         <author>Javitch JA</author>
         <author>Di Paolo G</author>
         <author>Chen EI</author>
         <author>Chan RB</author>
         <author>Carazo JM</author>
         <author>Area-Gomez E</author>
         <author>Jensen GJ</author>
         <author>Frank J</author>
         <author>Freyberg Z</author>
      </authors_list>
      <keywords>Ribosome, secretion, vesicle</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="false">
               <author order="1">Carter SD</author>
               <author order="2">Hampton CM</author>
               <author order="3">Langlois R</author>
               <author order="4">Grassucci RA</author>
               <author order="5">Farino ZJ</author>
               <author order="6">Morgenstern TM</author>
               <author order="7">Rice WJ</author>
               <author order="8">Velasco KR</author>
               <author order="9">Wigge C</author>
               <author order="10">Xu Y</author>
               <author order="11">Koller A</author>
               <author order="12">Melero R</author>
               <author order="13">Mitchell WG</author>
               <author order="14">Yi E</author>
               <author order="15">Aguilar JI</author>
               <author order="16">Levy ES</author>
               <author order="17">Greenberg NL</author>
               <author order="18">Li W</author>
               <author order="19">Courel M</author>
               <author order="20">Mahata SK</author>
               <author order="21">Freyberg R</author>
               <author order="22">Javitch JA</author>
               <author order="23">Di Paolo G</author>
               <author order="24">Chen EI</author>
               <author order="25">Chan RB</author>
               <author order="26">Carazo JM</author>
               <author order="27">Area-Gomez E</author>
               <author order="28">Jensen GJ</author>
               <author order="29">Frank J</author>
               <author order="30">Freyberg Z</author>
               <title>Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle</title>
               <journal>NAT.COMMUN.</journal>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Ribosome Associated Vesicle membrane-bound 80S ribosome</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Ribosome Associated Vesicle membrane-bound 80S ribosome</name>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name synonym="80S ribosome">Membrane-bound 80S ribosome</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="10116">Rattus norvegicus</organism>
               <synonym_organism>Rat</synonym_organism>
               <cell>INS-1E insulinoma cells</cell>
               <organelle>Ribosome Associated Vesicles</organelle>
               <cellular_location>Cytoplasm</cellular_location>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <molecular_weight>
               <experimental units="MDa">3</experimental>
               <theoretical units="MDa">3</theoretical>
            </molecular_weight>
            <ribosome-details>ribosome-eukaryote: ALL</ribosome-details>
         </complex_supramolecule>
      </supramolecule_list>
   </sample>
   <structure_determination_list>
      <structure_determination structure_determination_id="1">
         <method>subtomogramAveraging</method>
         <aggregation_state>cell</aggregation_state>
         <specimen_preparation_list>
            <subtomogram_averaging_preparation preparation_id="1">
               <grid>
                  <details>200 mesh gold grid with thin carbon support</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">150</chamber_temperature>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>Blot for 8 seconds before plunging</method>
               </vitrification>
            </subtomogram_averaging_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <subtomogram_averaging_microscopy microscopy_id="1">
               <microscope>FEI POLARA 300</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">2.26</nominal_cs>
               <nominal_defocus_min units="&#181;m">6.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">6.0</nominal_defocus_max>
               <nominal_magnification>15500.0</nominal_magnification>
               <calibrated_magnification>18977.0</calibrated_magnification>
               <specimen_holder_model>GATAN HELIUM</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">80</temperature_min>
                  <temperature_max units="K">93</temperature_max>
                  <temperature_average units="K">80</temperature_average>
               </temperature>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <details>Weak beam illumination</details>
               <date>2014-03-30</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                     <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <tilt_series>
                  <axis1>
                     <min_angle units="deg">-60</min_angle>
                     <max_angle units="deg">60</max_angle>
                  </axis1>
               </tilt_series>
            </subtomogram_averaging_microscopy>
         </microscopy_list>
         <subtomogram_averaging_processing image_processing_id="1">
            <details>The subtomograms were manually selected using the EMAN2 software package.</details>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>ETOMO/Serial, EM</name>
                  </software>
               </software_list>
               <details>Final maps were calculated from five averaged datasets</details>
               <number_subtomograms_used>1230</number_subtomograms_used>
            </final_reconstruction>
            <final_angle_assignment>
               <details>SPIDER: theta +/- 60 degrees</details>
            </final_angle_assignment>
         </subtomogram_averaging_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="41595">
      <file>emd_3405.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>220</col>
         <row>220</row>
         <sec>220</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>220</x>
         <y>220</y>
         <z>220</z>
      </spacing>
      <cell>
         <a units="&#8491;">576.39996</a>
         <b units="&#8491;">576.39996</b>
         <c units="&#8491;">576.39996</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>0.0</minimum>
         <maximum>122.880767820000003</maximum>
         <average>3.25539947</average>
         <std>11.725924490000001</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.62</x>
         <y units="&#8491;">2.62</y>
         <z units="&#8491;">2.62</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>12.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3405::::</details>
   </map>
</emd>