<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2409" 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>2013-07-02</deposition>
         <header_release>2013-07-31</header_release>
         <map_release>2013-10-30</map_release>
         <update>2014-10-22</update>
      </key_dates>
      <title>The architecture of yeast DNA polymerase 'zeta'. Electron microscopy reconstruction of the heterotetrameric complex Rev3-Rev7-Pol31-Pol32.</title>
      <authors_list>
         <author>Gomez-Llorente Y</author>
         <author>Malik R</author>
         <author>Jain R</author>
         <author>Roy Choudhury J</author>
         <author>Johnson RE</author>
         <author>Prakash L</author>
         <author>Prakash S</author>
         <author>Ubarretxena-Belandia I</author>
         <author>Aggarwal AK</author>
      </authors_list>
      <keywords>Translesion DNA synthesis, DNA repair, DNA replication, DNA polymerase zeta, genome integrity, cancer</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Gomez-Llorente Y</author>
               <author order="2">Malik R</author>
               <author order="3">Jain R</author>
               <author order="4">Roy Choudhury J</author>
               <author order="5">Johnson RE</author>
               <author order="6">Prakash L</author>
               <author order="7">Prakash S</author>
               <author order="8">Ubarretxena-Belandia I</author>
               <author order="9">Aggarwal AK</author>
               <title>The architecture of yeast DNA polymerase 'zeta'</title>
               <journal>CELL REP.</journal>
               <volume>5</volume>
               <first_page>79</first_page>
               <last_page>86</last_page>
               <year>2013</year>
               <external_references type="PUBMED">24120860</external_references>
               <external_references type="DOI">doi:10.1016/j.celrep.2013.08.046</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Polymerase Zeta heterotetramer of Saccharomyces cerevisiae</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Polymerase Zeta heterotetramer of Saccharomyces cerevisiae</name>
            <details>Rev3:Rev7:Pol31:Pol32N 1:1:1:1</details>
            <oligomeric_state>Heterotetramer</oligomeric_state>
            <number_unique_components>4</number_unique_components>
            <molecular_weight>
               <experimental units="MDa">0.3</experimental>
               <theoretical units="MDa">0.298</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="Rev7">DNA Polymerase 'Zeta' processivity subunit</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Baker's yeast</synonym_organism>
               <cellular_location>Cytoplasm</cellular_location>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.028</experimental>
               <theoretical units="MDa">0.028</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
               <recombinant_plasmid>PETDuet</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P38927</external_references>
               <external_references type="GO">GO:0070987</external_references>
               <external_references type="GO">GO:0042276</external_references>
               <external_references type="INTERPRO">IPR003511</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="Pol31">DNA Polymerase 'Delta' small subunit</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Baker's yeast</synonym_organism>
               <cellular_location>Cytoplasm</cellular_location>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.055</experimental>
               <theoretical units="MDa">0.055</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
               <recombinant_plasmid>PETDuet</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P46957</external_references>
               <external_references type="GO">GO:0043137</external_references>
               <external_references type="GO">GO:0006298</external_references>
               <external_references type="GO">GO:0006284</external_references>
               <external_references type="INTERPRO">IPR007185</external_references>
               <external_references type="INTERPRO">IPR024826</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="3">
            <name synonym="Pol32">DNA Polymerase 'Delta' subunit 3</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Baker's yeast</synonym_organism>
               <cellular_location>Cytoplasm</cellular_location>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.040</experimental>
               <theoretical units="MDa">0.040</theoretical>
            </molecular_weight>
            <details>We are using the N-terminal part of this protein. For further details, check the associated publication.</details>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
               <recombinant_plasmid>PETDuet</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P47110</external_references>
               <external_references type="GO">GO:0043137</external_references>
               <external_references type="GO">GO:0006298</external_references>
               <external_references type="GO">GO:0006284</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="4">
            <name synonym="Rev3">DNA Polymerase 'Zeta' catalytic subunit</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Baker's yeast</synonym_organism>
               <cellular_location>Cytoplasm</cellular_location>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.173</experimental>
               <theoretical units="MDa">0.173</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
               <recombinant_plasmid>PETDuet</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P14284</external_references>
               <external_references type="GO">GO:0070987</external_references>
               <external_references type="GO">GO:0042276</external_references>
               <external_references type="GO">GO:0006260</external_references>
               <external_references type="INTERPRO">IPR006172</external_references>
               <external_references type="INTERPRO">IPR017964</external_references>
               <external_references type="INTERPRO">IPR006133</external_references>
               <external_references type="INTERPRO">IPR006134</external_references>
               <external_references type="INTERPRO">IPR023211</external_references>
               <external_references type="INTERPRO">IPR012337</external_references>
               <external_references type="INTERPRO">IPR025687</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>8.0</ph>
                  <details>25mM Tris pH 8.0, 250mM NaCl</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>2 ul aliquots were adsorbed onto glow-discharged carbon coated copper grids, and negatively stained with 2% uranyl acetate.</details>
               </staining>
               <grid>
                  <details>Glow discharged carbon coated copper grids.</details>
               </grid>
               <vitrification>
                  <cryogen_name>NONE</cryogen_name>
                  <instrument>OTHER</instrument>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>JEOL 2100F</microscope>
               <illumination_mode>OTHER</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">2.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
               <nominal_magnification>40000.0</nominal_magnification>
               <calibrated_magnification>63450.0</calibrated_magnification>
               <specimen_holder_model>JEOL</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">80</temperature_min>
                  <temperature_max units="K">298</temperature_max>
                  <temperature_average units="K">293</temperature_average>
               </temperature>
               <date>2011-01-01</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC TVIPS</film_or_detector_model>
                     <average_electron_dose_per_image units="e/&#8491;^2">10</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <tilt_angle_min>0</tilt_angle_min>
               <tilt_angle_max>0</tilt_angle_max>
            </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>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">23.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>Xmipp, EMAN2, Spider</name>
                  </software>
               </software_list>
               <number_images_used>14844</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="2001">
      <file>emd_2409.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>80</col>
         <row>80</row>
         <sec>80</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>80</x>
         <y>80</y>
         <z>80</z>
      </spacing>
      <cell>
         <a units="&#8491;">302.4</a>
         <b units="&#8491;">302.4</b>
         <c units="&#8491;">302.4</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>-0.07746604</minimum>
         <maximum>0.19041532</maximum>
         <average>0.00239383</average>
         <std>0.02202785</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">3.78</x>
         <y units="&#8491;">3.78</y>
         <z units="&#8491;">3.78</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.0938</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Map of Pol-zeta-d heterotetramer by negative stain</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2409::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_2409.jpg</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>