<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2992" 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>2015-05-01</deposition>
         <header_release>2015-05-27</header_release>
         <map_release>2015-06-17</map_release>
         <update>2015-07-15</update>
      </key_dates>
      <title>Structure of a pre-catalytic retroviral Intasome bound to a human nucleosome</title>
      <authors_list>
         <author>Renault L</author>
         <author>Maskell D</author>
         <author>Cherepanov P</author>
         <author>Costa A</author>
      </authors_list>
      <keywords>retroviral integration, integrase, nucleosome</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Maskell D</author>
               <author order="2">Renault L</author>
               <author order="3">Serrao EA</author>
               <author order="4">Lesbats P</author>
               <author order="5">Matadeen R</author>
               <author order="6">Hare S</author>
               <author order="7">Lindemann D</author>
               <author order="8">Engelman AN</author>
               <author order="9">Costa A</author>
               <author order="10">Cherepanov P</author>
               <title>Structural basis for retroviral integration into nucleosomes</title>
               <journal>NATURE</journal>
               <volume>523</volume>
               <first_page>366</first_page>
               <last_page>369</last_page>
               <year>2015</year>
               <external_references type="PUBMED">26061770</external_references>
               <external_references type="DOI">doi:10.1038/nature14495</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>PFV intasome in complex with D02 nucleosome</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>PFV intasome in complex with D02 nucleosome</name>
            <number_unique_components>3</number_unique_components>
            <molecular_weight>
               <experimental units="MDa">0.390</experimental>
               <theoretical units="MDa">0.390</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>Intasome</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.399</experimental>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Heterodimer of 2 Nucleoprotein complexes (Intasome: 4 proteins + two 19bp DNA, Nucleosome: 8 proteins + 145bp DNA)</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
               <recombinant_plasmid>pET</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P14350</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name>Nucleosome</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>human</synonym_organism>
            </natural_source>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Heterodimer of 2 Nucleoprotein complexes (Intasome: 4 proteins + two 19bp DNA, Nucleosome: 8 proteins + 145bp DNA)</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
               <recombinant_plasmid>pet</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
         <dna macromolecule_id="3">
            <name>DNA</name>
            <natural_source database="NCBI">
               <organism ncbi="32630">synthetic construct</organism>
            </natural_source>
            <classification>DNA</classification>
            <structure>SINGLE STRANDED</structure>
            <synthetic_flag>true</synthetic_flag>
         </dna>
      </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">
               <concentration units="mg/mL">0.1</concentration>
               <buffer>
                  <ph>7.45</ph>
                  <details>320 mM NaCl, 25 mM BisTris propane-HCl</details>
               </buffer>
               <grid>
                  <details>400 mesh C-flat copper grids CF-1/1</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">80</chamber_humidity>
                  <chamber_temperature units="K">101</chamber_temperature>
                  <instrument>GATAN CRYOPLUNGE 3</instrument>
                  <method>The sample was incubated for 1 minute on the grid and blotted for 3.8 seconds before plunging.</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">2.7</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
               <nominal_magnification>59000.0</nominal_magnification>
               <calibrated_magnification>104500.0</calibrated_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <date>2013-10-08</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON I (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">14</sampling_interval>
                     </digitization_details>
                     <number_real_images>932</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                     <bits_per_pixel>32.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Particles were picked in Xmipp 3.0; Contrast Transfer Function was estimated using CTFFIND3. All further processing was performed within the RELION 1.2 environment.</details>
            <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;">7.8</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>RELION</name>
                  </software>
               </software_list>
               <number_images_used>53887</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="29414">
      <file>emd_2992.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>196</col>
         <row>196</row>
         <sec>196</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>196</x>
         <y>196</y>
         <z>196</z>
      </spacing>
      <cell>
         <a units="&#8491;">258.72</a>
         <b units="&#8491;">258.72</b>
         <c units="&#8491;">258.72</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>-0.45667186</minimum>
         <maximum>0.62969732</maximum>
         <average>0.00332227</average>
         <std>0.02546307</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.32</x>
         <y units="&#8491;">1.32</y>
         <z units="&#8491;">1.32</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.1</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of a pre-catalytic Intasome/Nucleosome complex</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2992::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_2992.png</file>
         </figure>
      </figure_list>
   </interpretation>
   <validation>
      <fsc_curve>
         <file>emd_2992_fsc.xml</file>
      </fsc_curve>
   </validation>
</emd>