<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3146" 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>2015-09-06</deposition>
         <header_release>2015-09-23</header_release>
         <map_release>2015-10-21</map_release>
         <update>2015-12-02</update>
      </key_dates>
      <title>Mechanism of eIF6 release from the nascent 60S ribosomal subunit</title>
      <authors_list>
         <author>Weis F</author>
         <author>Giudice E</author>
         <author>Churcher M</author>
         <author>Jin L</author>
         <author>Hilcenko C</author>
         <author>Wong CC</author>
         <author>Traynor D</author>
         <author>Kay RR</author>
         <author>Warren AJ</author>
      </authors_list>
      <keywords>ribosome, ribosomopathy, SBDS, cryo-EM, eIF6, Dictyostelium, EFL1, GTPase, ribosome biogenesis</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Weis F</author>
               <author order="2">Giudice E</author>
               <author order="3">Churcher M</author>
               <author order="4">Jin L</author>
               <author order="5">Hilcenko C</author>
               <author order="6">Wong CC</author>
               <author order="7">Traynor D</author>
               <author order="8">Kay RR</author>
               <author order="9">Warren AJ</author>
               <title>Mechanism of eIF6 release from the nascent 60S ribosomal subunit</title>
               <journal>NAT.STRUCT.MOL.BIOL.</journal>
               <volume>22</volume>
               <first_page>914</first_page>
               <last_page>919</last_page>
               <year>2015</year>
               <external_references type="PUBMED">26479198</external_references>
               <external_references type="DOI">doi:10.1038/NSMB.3112</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>5anb</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1</name>
            <number_unique_components>4</number_unique_components>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name>60S ribosomal subunit</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="44689">Dictyostelium discoideum</organism>
               <strain>HM2917</strain>
               <synonym_organism>Slime Mold</synonym_organism>
            </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: LSU 60S</ribosome-details>
         </complex_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="eIF6">Eukaryotic translation initiation factor 6</name>
            <natural_source database="NCBI">
               <organism ncbi="44689">Dictyostelium discoideum</organism>
               <strain>HM2917</strain>
               <synonym_organism>Slime Mold</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.026</experimental>
               <theoretical units="MDa">0.026</theoretical>
            </molecular_weight>
            <details>endogenous dictyostelium protein purified bound the 60S ribosomal subunit</details>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q551M2</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="SBDS">Shwachman-Bodian-Diamond syndrome protein</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.029</experimental>
               <theoretical units="MDa">0.029</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
               <recombinant_strain>C41</recombinant_strain>
               <recombinant_plasmid>pRSETA</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q9Y3A5</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="3">
            <name synonym="EFL1">Elongation factor-like 1</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.125</experimental>
               <theoretical units="MDa">0.125</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
               <recombinant_strain>BCY123</recombinant_strain>
               <recombinant_plasmid>pYES2</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q7Z2Z2</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">
               <buffer>
                  <ph>7.5</ph>
                  <details>50 mM HEPES-KOH, 100 mM K(CH3COO), 10 mM Mg(CH3COO)2, 6 mM beta-mercaptoethanol</details>
               </buffer>
               <grid>
                  <details>quantifoil R2/2 glow discharged</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">120</chamber_temperature>
                  <instrument>FEI VITROBOT MARK III</instrument>
                  <method>6.5s blot</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">300</acceleration_voltage>
               <nominal_cs units="mm">2.2</nominal_cs>
               <nominal_defocus_min units="&#181;m">2.2</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">2.8</nominal_defocus_max>
               <nominal_magnification>59000.0</nominal_magnification>
               <calibrated_magnification>105263.0</calibrated_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 59,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <date>2013-09-03</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                     <number_real_images>3844</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                     <details>Every image is the average of 16 frames recorded by the direct electron detector</details>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
            <single_particle_microscopy microscopy_id="2">
               <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_cs units="mm">2.2</nominal_cs>
               <nominal_defocus_min units="&#181;m">2.2</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">2.8</nominal_defocus_max>
               <nominal_magnification>59000.0</nominal_magnification>
               <calibrated_magnification>105263.0</calibrated_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 59,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <date>2013-09-06</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                     <number_real_images>3844</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                     <details>Every image is the average of 16 frames recorded by the direct electron detector</details>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">4.1</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>RELION</name>
                  </software>
               </software_list>
               <number_images_used>11970</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="105470">
      <file>emd_3146.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>300</col>
         <row>300</row>
         <sec>300</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>300</x>
         <y>300</y>
         <z>300</z>
      </spacing>
      <cell>
         <a units="&#8491;">399.0</a>
         <b units="&#8491;">399.0</b>
         <c units="&#8491;">399.0</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>-0.44422188</minimum>
         <maximum>0.64644915</maximum>
         <average>0.00301982</average>
         <std>0.02805543</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.33</x>
         <y units="&#8491;">1.33</y>
         <z units="&#8491;">1.33</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.06</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of 60S-eIF6-SBDS-EFL1 complex</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3146::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_3146.jpg</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>