<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2475" 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>2013-09-19</deposition>
         <header_release>2013-09-25</header_release>
         <map_release>2013-11-13</map_release>
         <update>2013-12-18</update>
      </key_dates>
      <title>Energy barriers and driving forces of tRNA translocation through the ribosome</title>
      <authors_list>
         <author>Bock LV</author>
         <author>Blau C</author>
         <author>Schroeder GF</author>
         <author>Davydov II</author>
         <author>Fischer N</author>
         <author>Stark H</author>
         <author>Rodnina MV</author>
         <author>Vaiana AC</author>
         <author>Grubmueller H</author>
      </authors_list>
      <keywords>Ribosome, translation, translocation, tRNA, molecular dynamics, simulation</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Bock LV</author>
               <author order="2">Blau C</author>
               <author order="3">Schroeder GF</author>
               <author order="4">Davydov II</author>
               <author order="5">Fischer N</author>
               <author order="6">Stark H</author>
               <author order="7">Rodnina MV</author>
               <author order="8">Vaiana AC</author>
               <author order="9">Grubmueller H</author>
               <title>Energy barriers and driving forces of tRNA translocation through the ribosome</title>
               <journal>NAT.STRUCT.MOL.BIOL.</journal>
               <volume>20</volume>
               <first_page>1390</first_page>
               <last_page>1396</last_page>
               <year>2013</year>
               <external_references type="PUBMED">24186064</external_references>
               <external_references type="DOI">doi:10.1038/nsmb.2690</external_references>
            </journal_citation>
         </primary_citation>
         <secondary_citation>
            <journal_citation published="true">
               <author order="1">Fischer N</author>
               <author order="2">Konevega AL</author>
               <author order="3">Wintermeyer W</author>
               <author order="4">Rodnina MV</author>
               <author order="5">Stark H</author>
               <title>Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy</title>
               <journal>NATURE</journal>
               <volume>466</volume>
               <first_page>329</first_page>
               <last_page>333</last_page>
               <year>2010</year>
               <external_references type="PUBMED">20631791</external_references>
               <external_references type="DOI">doi:10.1038/nature09206</external_references>
            </journal_citation>
         </secondary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>4v78</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Substrate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Substrate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)</name>
            <number_unique_components>4</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">2.5</theoretical>
            </molecular_weight>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name synonym="E. coli 70S">Ribosome</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="562">Escherichia coli</organism>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <molecular_weight>
               <theoretical units="MDa">2.5</theoretical>
            </molecular_weight>
            <ribosome-details>ribosome-prokaryote: ALL</ribosome-details>
         </complex_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <rna macromolecule_id="1">
            <name synonym="peptidyl tRNA">fMetVal-tRNAVal</name>
            <natural_source database="NCBI">
               <organism ncbi="562">Escherichia coli</organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.025</theoretical>
            </molecular_weight>
            <classification>TRANSFER</classification>
            <structure>DOUBLE HELIX</structure>
            <synthetic_flag>false</synthetic_flag>
         </rna>
         <rna macromolecule_id="2">
            <name synonym="deacylated tRNA">tRNAfMet</name>
            <natural_source database="NCBI">
               <organism ncbi="562">Escherichia coli</organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.025</theoretical>
            </molecular_weight>
            <classification>TRANSFER</classification>
            <structure>DOUBLE HELIX</structure>
            <synthetic_flag>false</synthetic_flag>
         </rna>
         <rna macromolecule_id="3">
            <name synonym="mRNA">m022 mRNA</name>
            <natural_source database="NCBI">
               <organism ncbi="32630">synthetic construct</organism>
            </natural_source>
            <details>Coding sequence AUGGUU</details>
            <classification>OTHER</classification>
            <structure>SINGLE STRANDED</structure>
            <synthetic_flag>true</synthetic_flag>
         </rna>
      </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>7.5</ph>
                  <details>50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine</details>
               </buffer>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">75</chamber_humidity>
                  <chamber_temperature units="K">77</chamber_temperature>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: Custom-built CEVS. Dew-point temperature (temperature on the grid) adjusted to 18 degrees C</details>
                  <timed_resolved_state>Samples were vitrified at different time points along the reaction coordinate (1, 2, 5 and 20 minutes after addition of deacylated tRNAfMet to 70S-fMetVal-tRNAVal complexes)</timed_resolved_state>
                  <method>Manual blotting for about 2 seconds</method>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI/PHILIPS CM200FEG</microscope>
               <illumination_mode>SPOT SCAN</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>FIELD EMISSION GUN</electron_source>
               <acceleration_voltage units="kV">160</acceleration_voltage>
               <nominal_cs units="mm">2.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
               <nominal_magnification>161000.0</nominal_magnification>
               <calibrated_magnification>162740.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <temperature>
                  <temperature_average units="K">77</temperature_average>
               </temperature>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 200,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <date>2007-01-02</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC TVIPS (4k x 4k)</film_or_detector_model>
                     <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Eucentric</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>local</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>IMAGIC, custom, Spider</name>
                  </software>
               </software_list>
               <details>Final maps were calculated from 13 datasets acquired at different time points, computationally sorted into distinct substrates</details>
               <number_images_used>5371</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="3457">
      <file>emd_2475.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>96</col>
         <row>96</row>
         <sec>96</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>96</x>
         <y>96</y>
         <z>96</z>
      </spacing>
      <cell>
         <a units="&#8491;">359.04</a>
         <b units="&#8491;">359.04</b>
         <c units="&#8491;">359.04</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>-162.02668761999999</minimum>
         <maximum>222.166534420000005</maximum>
         <average>0.00227879</average>
         <std>24.232742309999999</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">3.74</x>
         <y units="&#8491;">3.74</y>
         <z units="&#8491;">3.74</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>25.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2475::::</details>
   </map>
</emd>