<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2516" 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>2013-11-25</deposition>
         <header_release>2013-12-04</header_release>
         <map_release>2014-01-15</map_release>
         <update>2016-02-17</update>
      </key_dates>
      <title>ER membrane-associated ribosome from HeLa cells after treatment with Ribophorin I siRNA</title>
      <authors_list>
         <author>Pfeffer S</author>
         <author>Dudek J</author>
         <author>Gogala M</author>
         <author>Schorr S</author>
         <author>Linxweiler J</author>
         <author>Lang S</author>
         <author>Becker T</author>
         <author>Beckmann R</author>
         <author>Zimmermann R</author>
         <author>Foerster F</author>
      </authors_list>
      <keywords>endoplasmic reticulum, translocon, ribosome, oligosaccharyltransferase, OST, protein-conducting channel, Sec61, translocon-associated protein complex, TRAP</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Pfeffer S</author>
               <author order="2">Dudek J</author>
               <author order="3">Gogala M</author>
               <author order="4">Schorr S</author>
               <author order="5">Linxweiler J</author>
               <author order="6">Lang S</author>
               <author order="7">Becker T</author>
               <author order="8">Beckmann R</author>
               <author order="9">Zimmermann R</author>
               <author order="10">Foerster F</author>
               <title>Structure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon.</title>
               <journal>NAT.COMMUN.</journal>
               <volume>5</volume>
               <first_page>3072</first_page>
               <last_page>3072</last_page>
               <year>2014</year>
               <external_references type="PUBMED">24407213</external_references>
               <external_references type="DOI">doi:10.1038/ncomms4072</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>ER membrane-associated ribosome from HeLa cells after treatment with Ribophorin I siRNA</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>ER membrane-associated ribosome from HeLa cells after treatment with Ribophorin I siRNA</name>
            <number_unique_components>2</number_unique_components>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name>ER membrane-associated 80S ribosome</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <strain>HeLa</strain>
               <synonym_organism>Human</synonym_organism>
               <cellular_location>Endoplasmic reticulum</cellular_location>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <ribosome-details>ribosome-eukaryote: ALL</ribosome-details>
         </complex_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>ER protein translocon</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <strain>HeLa</strain>
               <synonym_organism>Human</synonym_organism>
               <cellular_location>Endoplasmic reticulum</cellular_location>
            </natural_source>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
      </macromolecule_list>
   </sample>
   <structure_determination_list>
      <structure_determination structure_determination_id="1">
         <method>subtomogramAveraging</method>
         <aggregation_state>particle</aggregation_state>
         <specimen_preparation_list>
            <subtomogram_averaging_preparation preparation_id="1">
               <concentration units="mg/mL">2</concentration>
               <grid>
                  <details>Lacey carbon molybdenum grid</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE-PROPANE MIXTURE</cryogen_name>
                  <chamber_humidity units="percentage">70</chamber_humidity>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>Blot 3 seconds before plunging.</method>
               </vitrification>
            </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_defocus_min units="&#181;m">7.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
               <nominal_magnification>29000.0</nominal_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <date>2012-07-10</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON I (4k x 4k)</film_or_detector_model>
                     <average_electron_dose_per_image units="e/&#8491;^2">60</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>Candidate particles were localized using template matching and cross correlation peaks in areas containing rough ER were visually inspected to identify true positive matches. At the selected coordinates, unbinned subtomograms were reconstructed individually from the weighted back-projections and aligned to a template.</details>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">40.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>av3, tom, PyTom</name>
                  </software>
               </software_list>
               <number_subtomograms_used>417</number_subtomograms_used>
            </final_reconstruction>
            <ctf_correction>
               <details>projection</details>
            </ctf_correction>
         </subtomogram_averaging_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="31251">
      <file>emd_2516.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>200</col>
         <row>200</row>
         <sec>200</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>200</x>
         <y>200</y>
         <z>200</z>
      </spacing>
      <cell>
         <a units="&#8491;">576.0</a>
         <b units="&#8491;">576.0</b>
         <c units="&#8491;">576.0</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>-6.25707579</minimum>
         <maximum>10.256055829999999</maximum>
         <average>0.0</average>
         <std>0.99999994</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.88</x>
         <y units="&#8491;">2.88</y>
         <z units="&#8491;">2.88</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.82</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>ER membrane-associated ribosome from HeLa cells after treatment with Ribophorin I siRNA</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2516::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_2516.tif</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>