<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2009" 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>2011-12-10</deposition>
         <header_release>2012-02-15</header_release>
         <map_release>2012-02-17</map_release>
         <update>2012-08-29</update>
      </key_dates>
      <title>3D reconstruction of an archaeal 70S ribosome in complex with aPelota and aABCE1</title>
      <authors_list>
         <author>Becker T</author>
         <author>Franckenberg S</author>
         <author>Wickles S</author>
         <author>Shoemaker CJ</author>
         <author>Anger AM</author>
         <author>Armache J-P</author>
         <author>Sieber H</author>
         <author>Ungewickell C</author>
         <author>Berninghausen O</author>
         <author>Daberkow I</author>
         <author>Karcher A</author>
         <author>Thomm M</author>
         <author>Hopfner K-P</author>
         <author>Green R</author>
         <author>Beckmann R</author>
      </authors_list>
      <keywords>translation, ribosome recycling, no-go mRNA decay,</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Becker T</author>
               <author order="2">Franckenberg S</author>
               <author order="3">Wickles S</author>
               <author order="4">Shoemaker CJ</author>
               <author order="5">Anger AM</author>
               <author order="6">Armache JP</author>
               <author order="7">Sieber H</author>
               <author order="8">Ungewickell C</author>
               <author order="9">Berninghausen O</author>
               <author order="10">Daberkow I</author>
               <author order="11">Karcher A</author>
               <author order="12">Thomm M</author>
               <author order="13">Hopfner KP</author>
               <author order="14">Green R</author>
               <author order="15">Beckmann R</author>
               <title>Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.</title>
               <journal>NATURE</journal>
               <volume>482</volume>
               <first_page>501</first_page>
               <last_page>506</last_page>
               <year>2012</year>
               <external_references type="PUBMED">22358840</external_references>
               <external_references type="DOI">doi:10.1038/nature10829</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>3j15</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1</name>
            <oligomeric_state>One 70S ribosome binds one aPelota and one aABCE1</oligomeric_state>
            <number_unique_components>3</number_unique_components>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name synonym="Pyrococcus furiosus 70S ribosome">Pyrococcus furiosus 70S ribosome</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="2261">Pyrococcus furiosus</organism>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <ribosome-details>ribosome-prokaryote: ALL</ribosome-details>
         </complex_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="ABCE1">aABCE1</name>
            <natural_source database="NCBI">
               <organism ncbi="2261">Pyrococcus furiosus</organism>
            </natural_source>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
            </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="Pelota">aPelota</name>
            <natural_source database="NCBI">
               <organism ncbi="311400">Thermococcus kodakarensis</organism>
            </natural_source>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
               <recombinant_plasmid>pET28</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               </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">
               <buffer>
                  <ph>8.199999999999999</ph>
                  <details>56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>cryo-EM</details>
               </staining>
               <grid>
                  <details>Quantifoil grids (3/3) with 2 nm carbon on top</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">95</chamber_humidity>
                  <instrument>OTHER</instrument>
                  <details>Vitrification instrument: Vitrobot</details>
                  <method>Blot for 10 seconds before plunging, use 2 layer of filter paper</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">200</acceleration_voltage>
               <nominal_cs units="mm">2.7</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.2</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.6</nominal_defocus_max>
               <nominal_magnification>75000.0</nominal_magnification>
               <specimen_holder_model>OTHER</specimen_holder_model>
               <details>Final magnification of the object on the CCD image is 148721</details>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">15.6</sampling_interval>
                     </digitization_details>
                     <number_real_images>10000</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                     <bits_per_pixel>16.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>autoloader</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Wiener Filter</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">6.6</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>SPIDER</name>
                  </software>
               </software_list>
               <details>sorting for ribosome conformation and ligand presence was performed</details>
               <number_images_used>51000</number_images_used>
            </final_reconstruction>
            <final_angle_assignment>
               <details>SPIDER</details>
            </final_angle_assignment>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="194673">
      <file>emd_2009.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>368</col>
         <row>368</row>
         <sec>368</sec>
      </dimensions>
      <origin>
         <col>-184</col>
         <row>-184</row>
         <sec>-183</sec>
      </origin>
      <spacing>
         <x>368</x>
         <y>368</y>
         <z>368</z>
      </spacing>
      <cell>
         <a units="&#8491;">455.4</a>
         <b units="&#8491;">455.4</b>
         <c units="&#8491;">455.4</c>
         <alpha units="deg">90.0</alpha>
         <beta units="deg">90.0</beta>
         <gamma units="deg">90.0</gamma>
      </cell>
      <axis_order>
         <fast>Y</fast>
         <medium>X</medium>
         <slow>Z</slow>
      </axis_order>
      <statistics>
         <minimum>-0.49689907</minimum>
         <maximum>0.74534863</maximum>
         <average>0.00440064</average>
         <std>0.04026932</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.2375</x>
         <y units="&#8491;">1.2375</y>
         <z units="&#8491;">1.2375</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.13</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>This is a 3D cryo-EM reconstruction of a Pyrococcus furiosus 70S ribosome in complex with aABCE1 and aPelota</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2009::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>3BK7</access_code>
               <chain>
                  <chain_id>A</chain_id>
               </chain>
            </initial_model>
            <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>MDFF</name>
               </software>
            </software_list>
            <details>PDBEntryID_givenInChain. Protocol: rigid body followed by molecular dynamics flexible fitting. rigid body fitting of individual domains followed by molecular dynamics flexible fitting</details>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>