<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3246" 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>2015-11-18</deposition>
         <header_release>2016-01-27</header_release>
         <map_release>2016-04-13</map_release>
         <update>2016-04-13</update>
      </key_dates>
      <title>Electron cryo-microscopy of Grapevine Fanleaf Virus complex with Nanobody</title>
      <authors_list>
         <author>Hemmer C</author>
         <author>Orlov I</author>
         <author>Ackerer L</author>
         <author>Marmonier A</author>
         <author>Hleibieh K</author>
         <author>Schmitt-Keichinger C</author>
         <author>Vigne E</author>
         <author>Gersch S</author>
         <author>Komar V</author>
         <author>Belval L</author>
         <author>Berthold F</author>
         <author>Monsion B</author>
         <author>Bron P</author>
         <author>Lemaire O</author>
         <author>Lorber B</author>
         <author>Sgro JY</author>
         <author>Gutierrez C</author>
         <author>Muyldermans S</author>
         <author>Demangeat G</author>
         <author>Klaholz BP</author>
         <author>Ritzenthaler C</author>
      </authors_list>
      <keywords>virus, nanobody, complex</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Hemmer C</author>
               <author order="2">Orlov I</author>
               <author order="3">Ackerer L</author>
               <author order="4">Marmonier A</author>
               <author order="5">Hleibieh K</author>
               <author order="6">Schmitt-Keichinger C</author>
               <author order="7">Vigne E</author>
               <author order="8">Gersch S</author>
               <author order="9">Komar V</author>
               <author order="10">Belval L</author>
               <author order="11">Berthold F</author>
               <author order="12">Monsion B</author>
               <author order="13">Bron P</author>
               <author order="14">Lemaire O</author>
               <author order="15">Lorber B</author>
               <author order="16">Sgro JY</author>
               <author order="17">Gutierrez C</author>
               <author order="18">Muyldermans S</author>
               <author order="19">Demangeat G</author>
               <author order="20">Klaholz BP</author>
               <author order="21">Ritzenthaler C</author>
               <title>Structural basis of Nanobody-mediated plant virus resistance and vector transmission revealed by cryo-EM.</title>
               <journal>To Be Published</journal>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>5foj</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Grapevine Fanleaf Virus complex with Nanobodies</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Grapevine Fanleaf Virus complex with Nanobodies</name>
            <number_unique_components>2</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name>Grapevine fanleaf virus</name>
            <details>Nanobodies were bound the virus surface.</details>
            <sci_species_name ncbi="12274">Grapevine fanleaf virus</sci_species_name>
            <natural_host database="NCBI">
               <organism>grapevine</organism>
               <synonym_organism>PLANTAE(HIGHER PLANTS)</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <triangulation>3</triangulation>
            </virus_shell>
            <virus_type>VIRION</virus_type>
            <virus_isolate>SPECIES</virus_isolate>
            <virus_enveloped>false</virus_enveloped>
            <virus_empty>false</virus_empty>
         </virus_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>Nanobody</name>
            <natural_source database="NCBI">
               <organism ncbi="32630">synthetic construct</organism>
            </natural_source>
            <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">
               <concentration units="mg/mL">0.5</concentration>
               <buffer>
                  <ph>8.300000000000001</ph>
                  <details>100 mM Tris pH 8.3, 50 mM NaCl.</details>
               </buffer>
               <grid>
                  <details>300 mesh 2/2 Quantifoil</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">95</chamber_humidity>
                  <instrument>FEI VITROBOT MARK III</instrument>
                  <method>blot for 2 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>OTHER</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>FIELD EMISSION GUN</electron_source>
               <acceleration_voltage units="kV">300</acceleration_voltage>
               <nominal_defocus_min units="&#181;m">0.6</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">6.0</nominal_defocus_max>
               <nominal_magnification>120000.0</nominal_magnification>
               <calibrated_magnification>120000.0</calibrated_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <date>2014-12-14</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>1055</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">50</average_electron_dose_per_image>
                     <details>Every image is the average of seven frames recorded by the direct electron detector.</details>
                     <bits_per_pixel>16.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Each Image</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">2.8</resolution>
               <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>Imagic</name>
                  </software>
               </software_list>
               <number_images_used>6139</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="221185">
      <file>emd_3246.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>384</col>
         <row>384</row>
         <sec>384</sec>
      </dimensions>
      <origin>
         <col>-192</col>
         <row>-192</row>
         <sec>-192</sec>
      </origin>
      <spacing>
         <x>384</x>
         <y>384</y>
         <z>384</z>
      </spacing>
      <cell>
         <a units="&#8491;">409.344</a>
         <b units="&#8491;">409.344</b>
         <c units="&#8491;">409.344</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>-9.91243362</minimum>
         <maximum>13.45023823</maximum>
         <average>0.0</average>
         <std>0.99999994</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.066</x>
         <y units="&#8491;">1.066</y>
         <z units="&#8491;">1.066</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>2.67</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Grapevine Fanleaf Virus reconstruction</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3246::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>4V5T</access_code>
            </initial_model>
            <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera, Coot</name>
               </software>
            </software_list>
            <details>iterative manual model building (Coot) and structure refinement (Phenix) against the cryo-EM map.</details>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
      <figure_list>
         <figure>
            <file>emd_3246.png</file>
         </figure>
         <figure>
            <file>emd_3246_1.png</file>
         </figure>
         <figure>
            <file>emd_3246_2.png</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>