<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2442" 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>2013-08-18</deposition>
         <header_release>2013-08-28</header_release>
         <map_release>2014-01-29</map_release>
         <update>2014-03-19</update>
      </key_dates>
      <title>Cryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human antibody 1F4</title>
      <authors_list>
         <author>Fibriansah G</author>
         <author>Tan JL</author>
         <author>de Alwis R</author>
         <author>Smith SA</author>
         <author>Ng T-S</author>
         <author>Kostyuchenko VA</author>
         <author>Ibarra KD</author>
         <author>Harris E</author>
         <author>de Silva A</author>
         <author>Crowe JE</author>
         <author>Lok S-M</author>
      </authors_list>
      <keywords>dengue virus, cryo-EM, structure, E proteins, human antibody, antibody, neutralization</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Fibriansah G</author>
               <author order="2">Tan JL</author>
               <author order="3">de Alwis R</author>
               <author order="4">Smith SA</author>
               <author order="5">Ng T-S</author>
               <author order="6">Kostyuchenko VA</author>
               <author order="7">Ibarra KD</author>
               <author order="8">Harris E</author>
               <author order="9">de Silva A</author>
               <author order="10">Crowe JE</author>
               <author order="11">Lok S-M</author>
               <title>A potent anti-dengue human antibody specifically recognizes the conformation of E protein monomers assembled on the virus surface</title>
               <journal>EMBO Mol. Med.</journal>
               <volume>6</volume>
               <first_page>358</first_page>
               <last_page>371</last_page>
               <year>2014</year>
               <external_references type="PUBMED">24421336</external_references>
               <external_references type="DOI">doi:10.1002/emmm.201303404</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>4c2i</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Dengue virus serotype 1 with Fab fragments of human monoclonal antibody 1F4</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Dengue virus serotype 1 with Fab fragments of human monoclonal antibody 1F4</name>
            <oligomeric_state>120 Fab molecules bind to one dengue virion</oligomeric_state>
            <number_unique_components>2</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name>Dengue virus 1</name>
            <details>strain PVP159</details>
            <sci_species_name ncbi="11053">Dengue virus 1</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>VERTEBRATES</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               <recombinant_organism ncbi="7160">Aedes albopictus</recombinant_organism>
               <recombinant_cell>C6/36</recombinant_cell>
            </host_system>
            <virus_type>VIRION</virus_type>
            <virus_isolate>SEROTYPE</virus_isolate>
            <virus_enveloped>true</virus_enveloped>
            <virus_empty>false</virus_empty>
            <sci_species_serotype>1</sci_species_serotype>
         </virus_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>Fab fragment of antibody 1F4</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.05</theoretical>
            </molecular_weight>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </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>8.0</ph>
                  <details>12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA</details>
               </buffer>
               <grid>
                  <details>ultra-thin carbon-coated lacey carbon grid</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">100</chamber_temperature>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>blot with filter paper for 2 s 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>SPOT SCAN</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">1.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
               <nominal_magnification>47000.0</nominal_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <temperature>
                  <temperature_average units="K">100</temperature_average>
               </temperature>
               <date>2012-09-14</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON I (4k x 4k)</film_or_detector_model>
                     <number_real_images>254</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">17.5</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>The particles were selected manually.</details>
            <ctf_correction>
               <details>Each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">6.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN, MPSA</name>
                  </software>
               </software_list>
               <number_images_used>10270</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="1024001">
      <file>emd_2442.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>640</col>
         <row>640</row>
         <sec>640</sec>
      </dimensions>
      <origin>
         <col>-320</col>
         <row>-320</row>
         <sec>-320</sec>
      </origin>
      <spacing>
         <x>640</x>
         <y>640</y>
         <z>640</z>
      </spacing>
      <cell>
         <a units="&#8491;">640.0</a>
         <b units="&#8491;">640.0</b>
         <c units="&#8491;">640.0</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>-0.76943427</minimum>
         <maximum>12.091775889999999</maximum>
         <average>0.0</average>
         <std>0.99999994</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.0</x>
         <y units="&#8491;">1.0</y>
         <z units="&#8491;">1.0</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>2.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Cryo-EM reconstruction of Dengue virus serotype 1 complexed with Fab fragments of human antibody 1F4</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2442::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_2442.tiff</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>